Variant report

Variant	rs60247651
Chromosome Location	chr3:50272953-50272954
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:12)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:12 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PML	chr3:50272939-50274065	GM12878	blood:	n/a	n/a
2	POLR2A	chr3:50272949-50273881	SK-N-SH	brain:	n/a	n/a
3	MTA3	chr3:50272927-50273462	GM12878	blood:	n/a	n/a
4	POLR2A	chr3:50272928-50274059	GM12892	blood:	n/a	n/a
5	RFX5	chr3:50272897-50274222	IMR90	lung:	n/a	chr3:50273499-50273508
6	HCFC1	chr3:50272778-50276694	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr3:50272842-50274979	IMR90	lung:	n/a	n/a
8	POLR2A	chr3:50272916-50275952	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr3:50272843-50274733	HepG2	liver:	n/a	n/a
10	TBP	chr3:50272943-50273889	K562	blood:	n/a	n/a
11	POLR2A	chr3:50272935-50273360	PFSK-1	brain:	n/a	n/a
12	ESRRA	chr3:50272846-50274401	GM12878	blood:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50272477..50276068-chr3:50288828..50297512,10	MCF-7	breast:
2	chr3:50272229..50274587-chr3:50373396..50376334,2	MCF-7	breast:
3	chr3:50271160..50275227-chr3:50277363..50285143,16	MCF-7	breast:
4	chr3:50272542..50276085-chr3:50328223..50330525,3	MCF-7	breast:
5	chr3:50263557..50265645-chr3:50272051..50275116,5	K562	blood:
6	chr3:50271706..50275857-chr3:50303511..50313889,17	MCF-7	breast:
7	chr3:50225100..50230290-chr3:50272107..50276590,4	MCF-7	breast:
8	chr3:50272615..50275191-chr3:50335158..50337593,2	MCF-7	breast:
9	chr3:50272452..50275619-chr3:50295837..50299163,4	MCF-7	breast:
10	chr3:50272666..50274549-chr3:50296154..50297736,2	K562	blood:
11	chr3:50272604..50274758-chr3:50646990..50649583,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GNAT1-2	chr3:50272696-50272999	l_2364_chr3:50272695-50274883_testes

No data

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000213600	TF binding region
ENSG00000114353	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000232352	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000114737	Chromatin interaction
ENSG00000230454	Chromatin interaction
ENSG00000068028	Chromatin interaction
ENSG00000114349	Chromatin interaction
ENSG00000214706	Chromatin interaction
ENSG00000186792	Chromatin interaction
ENSG00000243477	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10510755	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12635953	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2071802	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2071803	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2073498	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2097247	0.90[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2236939	0.85[EUR][1000 genomes]
rs2239801	0.84[EUR][1000 genomes]
rs2301639	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28365992	0.87[EUR][1000 genomes]
rs3755832	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3806708	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs41291724	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs45536634	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57319506	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57462170	0.87[EUR][1000 genomes]
rs58051625	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][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:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50265600-50273000	Weak transcription	Right Atrium	heart
2	chr3:50265800-50273000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:50266200-50273000	Weak transcription	Fetal Stomach	stomach
4	chr3:50266400-50273000	Weak transcription	Fetal Brain Female	brain
5	chr3:50266400-50273200	Weak transcription	NHLF	lung
6	chr3:50266400-50273400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr3:50266600-50273000	Weak transcription	NHEK	skin
8	chr3:50266800-50273000	Weak transcription	Brain Germinal Matrix	brain
9	chr3:50267600-50273600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:50268000-50273000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr3:50268200-50273600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr3:50268600-50273000	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr3:50268600-50273000	Weak transcription	Brain Angular Gyrus	brain
14	chr3:50268600-50273000	Weak transcription	Brain Substantia Nigra	brain
15	chr3:50268600-50273000	Weak transcription	HSMM	muscle
16	chr3:50268600-50273600	Weak transcription	NHDF-Ad	bronchial
17	chr3:50268800-50273000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr3:50268800-50273000	Weak transcription	Osteobl	bone
19	chr3:50270400-50273000	Enhancers	K562	blood
20	chr3:50270800-50273000	Enhancers	Hela-S3	cervix
21	chr3:50271200-50273000	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:50271200-50273000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:50271200-50273000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr3:50271200-50273000	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr3:50271200-50273600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:50271200-50273600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:50271400-50273000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:50271400-50273000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr3:50271400-50273000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr3:50271400-50273000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr3:50271800-50273000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr3:50271800-50273000	Enhancers	Duodenum Mucosa	Duodenum
33	chr3:50272000-50273000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:50272000-50273000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr3:50272000-50273000	Enhancers	Primary B cells from cord blood	blood
36	chr3:50272000-50273000	Enhancers	Primary B cells from peripheral blood	blood
37	chr3:50272000-50273000	Enhancers	Primary T cells fromperipheralblood	blood
38	chr3:50272000-50273000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr3:50272000-50273000	Enhancers	Fetal Muscle Leg	muscle
40	chr3:50272000-50273000	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr3:50272000-50273000	Enhancers	HepG2	liver
42	chr3:50272000-50273200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr3:50272000-50273200	Enhancers	Fetal Heart	heart
44	chr3:50272000-50273200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr3:50272000-50273400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
46	chr3:50272000-50273600	Enhancers	Primary hematopoietic stem cells	blood
47	chr3:50272000-50273600	Enhancers	Stomach Mucosa	stomach
48	chr3:50272200-50273000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr3:50272200-50273000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:50272200-50273000	Enhancers	Brain Hippocampus Middle	brain

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