Variant report

Variant	rs9867538
Chromosome Location	chr3:50259209-50259210
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr3:50259133-50259614	H1-hESC	embryonic stem cell:	n/a	chr3:50259417-50259438 chr3:50259422-50259440
2	FOSL2	chr3:50258504-50259944	HepG2	liver:	n/a	n/a
3	MBD4	chr3:50259145-50259647	HepG2	liver:	n/a	n/a
4	RAD21	chr3:50259200-50259648	H1-hESC	embryonic stem cell:	n/a	chr3:50259422-50259434 chr3:50259420-50259439 chr3:50259423-50259436 chr3:50259585-50259594
5	CEBPD	chr3:50259112-50259674	HepG2	liver:	n/a	n/a
6	POLR2A	chr3:50258479-50260223	HepG2	liver:	n/a	n/a
7	RAD21	chr3:50259132-50259701	HepG2	liver:	n/a	chr3:50259422-50259434 chr3:50259420-50259439 chr3:50259423-50259436 chr3:50259585-50259594
8	TBP	chr3:50259207-50259531	H1-hESC	embryonic stem cell:	n/a	n/a
9	CREB1	chr3:50259147-50259719	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr3:50258907-50259472	HepG2	liver:	n/a	n/a
11	POLR2A	chr3:50256305-50260044	HepG2	liver:	n/a	n/a
12	POLR2A	chr3:50258509-50259799	HepG2	liver:	n/a	n/a
13	CTCF	chr3:50259193-50259591	HepG2	liver:	n/a	chr3:50259417-50259438 chr3:50259422-50259440
14	RCOR1	chr3:50259155-50259498	HepG2	liver:	n/a	n/a
15	POLR2A	chr3:50258547-50259879	HepG2	liver:	n/a	n/a
16	ARID3A	chr3:50258712-50259556	HepG2	liver:	n/a	n/a
17	RAD21	chr3:50259113-50259606	HepG2	liver:	n/a	chr3:50259422-50259434 chr3:50259420-50259439 chr3:50259423-50259436 chr3:50259585-50259594
18	FOXA1	chr3:50258615-50259742	HepG2	liver:	n/a	n/a
19	CHD2	chr3:50259027-50259964	HepG2	liver:	n/a	n/a
20	HEY1	chr3:50259134-50259571	HepG2	liver:	n/a	n/a
21	POLR2A	chr3:50258902-50259864	HepG2	liver:	n/a	n/a
22	HEY1	chr3:50258532-50259797	HepG2	liver:	n/a	n/a
23	POLR2A	chr3:50259198-50259414	H1-hESC	embryonic stem cell:	n/a	n/a
24	RAD21	chr3:50259108-50259640	HepG2	liver:	n/a	chr3:50259422-50259434 chr3:50259420-50259439 chr3:50259423-50259436 chr3:50259585-50259594
25	POLR2A	chr3:50258720-50259817	HepG2	liver:	n/a	n/a
26	YY1	chr3:50259202-50259832	HepG2	liver:	n/a	n/a
27	RAD21	chr3:50259119-50259742	HCT-116	colon:	n/a	chr3:50259422-50259434 chr3:50259420-50259439 chr3:50259423-50259436 chr3:50259585-50259594
28	CTCF	chr3:50259158-50259642	H1-hESC	embryonic stem cell:	n/a	chr3:50259417-50259438 chr3:50259422-50259440
29	MYBL2	chr3:50258987-50259719	HepG2	liver:	n/a	n/a
30	MYBL2	chr3:50259100-50259663	HepG2	liver:	n/a	n/a
31	MBD4	chr3:50258687-50259828	HepG2	liver:	n/a	n/a
32	CTCF	chr3:50259138-50259654	K562	blood:	n/a	chr3:50259417-50259438 chr3:50259422-50259440
33	CTCF	chr3:50259200-50259644	HepG2	liver:	n/a	chr3:50259417-50259438 chr3:50259422-50259440
34	HNF4A	chr3:50258686-50259614	HepG2	liver:	n/a	chr3:50258970-50258978 chr3:50258851-50258859 chr3:50259487-50259494 chr3:50258844-50258859 chr3:50258969-50258984
35	HDAC2	chr3:50259168-50259603	HepG2	liver:	n/a	n/a
36	GABPA	chr3:50259191-50259652	H1-hESC	embryonic stem cell:	n/a	n/a
37	RAD21	chr3:50259079-50259661	H1-hESC	embryonic stem cell:	n/a	chr3:50259422-50259434 chr3:50259420-50259439 chr3:50259423-50259436 chr3:50259585-50259594
38	NFIC	chr3:50258869-50259567	HepG2	liver:	n/a	chr3:50258925-50258953

No.	Distal block	Cell Line	Cell type
1	chr3:50258222..50260733-chr3:50266764..50268364,2	K562	blood:
2	chr3:50253527..50255609-chr3:50256961..50261063,4	K562	blood:
3	chr3:50237804..50240156-chr3:50257225..50259913,2	K562	blood:

Variant related genes	Relation type
GNAI2	TF binding region
ENSG00000188338	Chromatin interaction
ENSG00000114353	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs4141407	0.91[AFR][1000 genomes]
rs7611366	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9847853	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:31 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834690	chr3:50101835-50267584	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers 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	24 gene(s)	inside rSNPs	diseases
2	nsv515986	chr3:50104307-50267584	Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS 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	24 gene(s)	inside rSNPs	diseases
3	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
4	nsv876768	chr3:50144951-50267584	Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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
29	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
30	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
31	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:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50244000-50263800	Weak transcription	Right Atrium	heart
2	chr3:50244200-50263800	Weak transcription	Left Ventricle	heart
3	chr3:50244400-50263800	Weak transcription	Right Ventricle	heart
4	chr3:50247400-50264400	Weak transcription	Ovary	ovary
5	chr3:50251600-50263600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr3:50251800-50263400	Weak transcription	Fetal Brain Female	brain
7	chr3:50251800-50263800	Weak transcription	Brain Angular Gyrus	brain
8	chr3:50253000-50260000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr3:50255400-50263800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr3:50255600-50259600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:50256400-50263800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:50257400-50259400	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr3:50257400-50259600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr3:50257400-50259600	Enhancers	Fetal Intestine Large	intestine
15	chr3:50257400-50259600	Enhancers	Fetal Intestine Small	intestine
16	chr3:50257400-50259800	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:50257600-50259600	Enhancers	Fetal Thymus	thymus
18	chr3:50257600-50259800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:50257600-50259800	Enhancers	Brain Substantia Nigra	brain
20	chr3:50257800-50259600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr3:50257800-50259600	Enhancers	Primary hematopoietic stem cells	blood
22	chr3:50257800-50259600	Enhancers	Liver	Liver
23	chr3:50257800-50259800	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:50257800-50259800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr3:50258000-50259600	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr3:50258000-50259600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr3:50258000-50259600	Enhancers	Fetal Stomach	stomach
28	chr3:50258000-50263600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr3:50258200-50259600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr3:50258200-50259600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr3:50258200-50263600	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr3:50258400-50263400	Weak transcription	Fetal Lung	lung
33	chr3:50258600-50259800	Flanking Active TSS	HepG2	liver
34	chr3:50258800-50259400	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:50258800-50259400	Weak transcription	Brain Germinal Matrix	brain
36	chr3:50259000-50259400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:50259000-50259600	Enhancers	HUES6 Cell Line	embryonic stem cell
38	chr3:50259000-50259600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:50259000-50259600	Weak transcription	Fetal Brain Male	brain
40	chr3:50259000-50259800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr3:50259000-50259800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr3:50259000-50259800	Enhancers	Pancreas	Pancrea
43	chr3:50259000-50259800	Enhancers	Psoas Muscle	Psoas
44	chr3:50259000-50259800	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:50259200-50259400	Enhancers	Small Intestine	intestine
46	chr3:50259200-50259600	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr3:50259200-50259600	Enhancers	Brain Hippocampus Middle	brain
48	chr3:50259200-50259800	Enhancers	Brain Anterior Caudate	brain
49	chr3:50259200-50259800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr3:50259200-50263400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--

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