Variant report

Variant	rs62260798
Chromosome Location	chr3:50274278-50274279
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:50273031-50276027	Raji	blood:	n/a	n/a
2	BRCA1	chr3:50274208-50274441	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr3:50273008-50275998	GM12891	blood:	n/a	n/a
4	POLR2A	chr3:50274276-50276539	U87	brain:	n/a	n/a
5	STAT5A	chr3:50273531-50274302	GM12878	blood:	n/a	n/a
6	SIN3A	chr3:50273106-50274858	H1-hESC	embryonic stem cell:	n/a	chr3:50273585-50273598
7	POLR2A	chr3:50274273-50275874	HUVEC	blood vessel:	n/a	n/a
8	HCFC1	chr3:50272778-50276694	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr3:50274269-50274848	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr3:50273115-50276460	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr3:50272972-50276523	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr3:50273046-50275872	GM18505	blood:	n/a	n/a
13	MXI1	chr3:50272842-50274979	IMR90	lung:	n/a	n/a
14	POLR2A	chr3:50273150-50274824	MCF10A-Er-Src	breast:	n/a	n/a
15	POLR2A	chr3:50272916-50275952	SK-N-MC	brain:	n/a	n/a
16	POLR2A	chr3:50272843-50274733	HepG2	liver:	n/a	n/a
17	POLR2A	chr3:50272988-50274725	K562	blood:	n/a	n/a
18	ZNF263	chr3:50273202-50276181	HEK293-T-REx	kidney:	n/a	chr3:50275458-50275467
19	MXI1	chr3:50272978-50276384	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr3:50274276-50276727	U87	brain:	n/a	n/a
21	POLR2A	chr3:50273123-50274871	H1-hESC	embryonic stem cell:	n/a	n/a
22	REST	chr3:50273218-50274750	H1-neurons	neurons:	n/a	chr3:50274704-50274717 chr3:50274003-50274016
23	MTA3	chr3:50273712-50276297	GM12878	blood:	n/a	n/a
24	SMARCB1	chr3:50273205-50276456	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr3:50273029-50276147	GM12878	blood:	n/a	n/a
26	POLR2A	chr3:50272998-50277892	HUVEC	blood vessel:	n/a	n/a
27	WRNIP1	chr3:50273856-50276216	GM12878	blood:	n/a	n/a
28	CHD1	chr3:50273218-50275777	GM12878	blood:	n/a	chr3:50273588-50273598 chr3:50274283-50274290
29	POLR2A	chr3:50273070-50275799	GM12892	blood:	n/a	n/a
30	MAZ	chr3:50272993-50276585	IMR90	lung:	n/a	n/a
31	ESRRA	chr3:50272846-50274401	GM12878	blood:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48514041..48514610-chr3:50273546..50274395,2	Hela-S3	cervix:
2	chr3:50273556..50275269-chr3:50364690..50367393,2	MCF-7	breast:
3	chr3:50273339..50275012-chr3:50356233..50359158,2	K562	blood:
4	chr3:50273331..50275965-chr3:50307293..50309702,3	K562	blood:
5	chr3:50192501..50194771-chr3:50274192..50275707,2	MCF-7	breast:
6	chr3:50273482..50276230-chr3:50357348..50359283,2	MCF-7	breast:
7	chr3:50272477..50276068-chr3:50288828..50297512,10	MCF-7	breast:
8	chr3:50272229..50274587-chr3:50373396..50376334,2	MCF-7	breast:
9	chr3:50271160..50275227-chr3:50277363..50285143,16	MCF-7	breast:
10	chr3:50273788..50275475-chr3:50353006..50355961,2	MCF-7	breast:
11	chr3:50272542..50276085-chr3:50328223..50330525,3	MCF-7	breast:
12	chr3:50263557..50265645-chr3:50272051..50275116,5	K562	blood:
13	chr3:50273624..50275186-chr3:50358650..50361013,3	MCF-7	breast:
14	chr3:50271706..50275857-chr3:50303511..50313889,17	MCF-7	breast:
15	chr3:50225100..50230290-chr3:50272107..50276590,4	MCF-7	breast:
16	chr3:50272615..50275191-chr3:50335158..50337593,2	MCF-7	breast:
17	chr3:50274207..50276620-chr3:50314026..50316951,2	MCF-7	breast:
18	chr3:50273437..50275421-chr3:50288351..50290514,2	MCF-7	breast:
19	chr3:50272452..50275619-chr3:50295837..50299163,4	MCF-7	breast:
20	chr3:50273459..50274335-chr3:50283505..50284344,2	K562	blood:
21	chr3:50272666..50274549-chr3:50296154..50297736,2	K562	blood:
22	chr3:50272604..50274758-chr3:50646990..50649583,2	K562	blood:
23	chr3:50149717..50151316-chr3:50273425..50276151,2	MCF-7	breast:
24	chr3:50273529..50275833-chr3:50328515..50330856,2	K562	blood:

(count:1 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNAT1-2	chr3:50273569-50274883	l_2364_chr3:50272695-50274883_testes

No data

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000213600	TF binding region
ENSG00000186792	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000114353	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000001617	Chromatin interaction
ENSG00000179564	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000235016	Chromatin interaction
ENSG00000114383	Chromatin interaction
ENSG00000003756	Chromatin interaction
ENSG00000243477	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000068001	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000114349	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12486832	1.00[AFR][1000 genomes]
rs12636449	0.82[EUR][1000 genomes]
rs60429865	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62260773	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs62260792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62260813	1.00[AFR][1000 genomes]
rs62260817	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001775	chr3:50129479-50311666	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
3	nsv1013949	chr3:50151712-50339163	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
4	nsv590250	chr3:50153356-50332697	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv876769	chr3:50155468-50408398	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
6	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
7	esv1793751	chr3:50157364-50476363	Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
8	esv1828162	chr3:50157364-50506151	Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv590251	chr3:50158774-50337422	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
10	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
11	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
12	nsv523560	chr3:50172397-50339163	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
13	nsv460529	chr3:50178011-50324672	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
14	nsv460530	chr3:50178011-50324672	Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
15	nsv590252	chr3:50178011-50324672	Enhancers Bivalent Enhancer Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
16	nsv1002916	chr3:50187646-50311666	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
17	nsv536564	chr3:50187646-50311666	Flanking Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
18	nsv1014256	chr3:50187646-50339163	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
19	nsv536565	chr3:50187646-50339163	Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
20	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
21	nsv590253	chr3:50196418-50337422	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
22	esv2757870	chr3:50198478-50371377	Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
23	esv2759148	chr3:50198478-50371377	Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
24	nsv834692	chr3:50198485-50393464	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
25	nsv590254	chr3:50243510-50388607	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
26	nsv460531	chr3:50247824-50436827	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
27	nsv590255	chr3:50247824-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
28	nsv876772	chr3:50255305-50436827	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50272800-50274600	Active TSS	Brain Anterior Caudate	brain
2	chr3:50272800-50275200	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:50272800-50275600	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr3:50272800-50275800	Active TSS	iPS-15b Cell Line	embryonic stem cell
5	chr3:50272800-50275800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr3:50272800-50275800	Active TSS	GM12878-XiMat	blood
7	chr3:50272800-50276000	Active TSS	Psoas Muscle	Psoas
8	chr3:50273000-50274400	Active TSS	Rectal Smooth Muscle	rectum
9	chr3:50273000-50274400	Active TSS	A549	lung
10	chr3:50273000-50274400	Active TSS	NHEK	skin
11	chr3:50273000-50274600	Active TSS	Brain Hippocampus Middle	brain
12	chr3:50273000-50274800	Active TSS	Brain Substantia Nigra	brain
13	chr3:50273000-50274800	Active TSS	Fetal Intestine Large	intestine
14	chr3:50273000-50275000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:50273000-50275200	Active TSS	Osteobl	bone
16	chr3:50273000-50275400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr3:50273000-50275600	Active TSS	HUES6 Cell Line	embryonic stem cell
18	chr3:50273000-50275600	Active TSS	Breast Myoepithelial Primary Cells	Breast
19	chr3:50273000-50275600	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr3:50273000-50275600	Active TSS	Colon Smooth Muscle	Colon
21	chr3:50273000-50275600	Active TSS	Right Atrium	heart
22	chr3:50273000-50275800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr3:50273000-50275800	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr3:50273000-50275800	Active TSS	HUES64 Cell Line	embryonic stem cell
25	chr3:50273000-50275800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:50273000-50275800	Active TSS	Primary T cells from cord blood	blood
27	chr3:50273000-50275800	Active TSS	Fetal Lung	lung
28	chr3:50273000-50275800	Active TSS	HSMMtube	muscle
29	chr3:50273000-50276000	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:50273000-50276000	Active TSS	H9 Cell Line	embryonic stem cell
31	chr3:50273000-50276000	Active TSS	Aorta	Aorta
32	chr3:50273000-50276000	Active TSS	Fetal Kidney	kidney
33	chr3:50273000-50276000	Active TSS	Ovary	ovary
34	chr3:50273000-50276400	Active TSS	Pancreatic Islets	Pancreatic Islet
35	chr3:50273200-50274400	Active TSS	H1 Cell Line	embryonic stem cell
36	chr3:50273200-50274400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr3:50273200-50274400	Active TSS	Brain Cingulate Gyrus	brain
38	chr3:50273200-50274600	Active TSS	Fetal Intestine Small	intestine
39	chr3:50273200-50274800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr3:50273200-50275200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr3:50273200-50275400	Active TSS	HMEC	breast
42	chr3:50273200-50275600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr3:50273200-50275600	Active TSS	Primary monocytes fromperipheralblood	blood
44	chr3:50273200-50275600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:50273200-50275600	Active TSS	Primary T helper naive cells from peripheral blood	blood
46	chr3:50273200-50275600	Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr3:50273200-50275600	Active TSS	Primary T killer naive cells fromperipheralblood	blood
48	chr3:50273200-50275600	Active TSS	Muscle Satellite Cultured Cells	--
49	chr3:50273200-50275600	Active TSS	Thymus	Thymus
50	chr3:50273200-50275600	Active TSS	Hela-S3	cervix

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