Variant report

Variant	rs9836046
Chromosome Location	chr3:50288462-50288463
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RCOR1	chr3:50288325-50289284	IMR90	lung:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:50288085..50289817-chr3:50297461..50299004,2	K562	blood:
2	chr3:50276446..50277963-chr3:50288169..50290454,2	MCF-7	breast:
3	chr3:50286473..50289840-chr3:50357894..50361890,3	MCF-7	breast:
4	chr3:50283028..50285015-chr3:50286651..50289261,2	MCF-7	breast:
5	chr3:50263658..50265512-chr3:50286295..50288716,2	K562	blood:
6	chr3:50288326..50289923-chr3:50306596..50308969,2	MCF-7	breast:
7	chr3:50273437..50275421-chr3:50288351..50290514,2	MCF-7	breast:

No data

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000230454	Chromatin interaction
ENSG00000068001	Chromatin interaction
ENSG00000213600	Chromatin interaction
ENSG00000012171	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11916258	0.87[EUR][1000 genomes]
rs1894324	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2236944	0.90[AFR][1000 genomes]
rs2298954	0.82[AFR][1000 genomes]
rs35742391	0.95[EUR][1000 genomes]
rs57453427	0.95[EUR][1000 genomes]
rs6768830	0.95[EUR][1000 genomes]
rs7636862	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7641224	0.95[EUR][1000 genomes]
rs886075	0.95[EUR][1000 genomes]
rs9851719	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9875873	0.95[EUR][1000 genomes]
rs9878345	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50276400-50294400	Genic enhancers	Lung	lung
2	chr3:50283400-50293200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:50283800-50289000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:50283800-50289400	Enhancers	Left Ventricle	heart
5	chr3:50283800-50294000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:50284000-50289000	Enhancers	Brain Cingulate Gyrus	brain
7	chr3:50284000-50289200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr3:50284000-50289400	Genic enhancers	Primary B cells from peripheral blood	blood
9	chr3:50284200-50288600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr3:50284200-50289600	Genic enhancers	Duodenum Smooth Muscle	Duodenum
11	chr3:50284200-50289600	Enhancers	Right Atrium	heart
12	chr3:50284200-50289800	Enhancers	Stomach Mucosa	stomach
13	chr3:50284200-50297000	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr3:50284400-50289400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr3:50284400-50289400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr3:50284400-50290800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr3:50284400-50292000	Weak transcription	Fetal Brain Male	brain
18	chr3:50284400-50293000	Genic enhancers	Primary T cells fromperipheralblood	blood
19	chr3:50284400-50295000	Genic enhancers	Spleen	Spleen
20	chr3:50284400-50295800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr3:50284400-50297000	Genic enhancers	Fetal Muscle Leg	muscle
22	chr3:50284600-50288600	Enhancers	Duodenum Mucosa	Duodenum
23	chr3:50284600-50289400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:50284600-50294000	Genic enhancers	Placenta	Placenta
25	chr3:50284800-50288800	Enhancers	Liver	Liver
26	chr3:50284800-50289800	Genic enhancers	Primary T helper cells PMA-I stimulated	--
27	chr3:50284800-50291000	Weak transcription	HepG2	liver
28	chr3:50284800-50291200	Strong transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:50284800-50293000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
30	chr3:50284800-50294000	Weak transcription	Fetal Kidney	kidney
31	chr3:50284800-50300600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr3:50285000-50289000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr3:50285000-50290600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
34	chr3:50285200-50288600	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr3:50285200-50288600	Weak transcription	K562	blood
36	chr3:50285200-50289000	Genic enhancers	Colon Smooth Muscle	Colon
37	chr3:50285200-50290800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
38	chr3:50285200-50294400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:50285200-50296000	Strong transcription	Dnd41	blood
40	chr3:50285200-50296600	Strong transcription	Thymus	Thymus
41	chr3:50285400-50288800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr3:50285600-50289000	Enhancers	HUVEC	blood vessel
43	chr3:50285600-50289800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:50285800-50288600	Enhancers	Brain Anterior Caudate	brain
45	chr3:50285800-50289000	Enhancers	Fetal Heart	heart
46	chr3:50286000-50289000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:50286000-50293000	Genic enhancers	HSMM	muscle
48	chr3:50286000-50293400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr3:50286000-50296200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr3:50286200-50289600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain

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