Variant report

Variant	rs10975646
Chromosome Location	chr9:6566401-6566402
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	GATA2	chr9:6566400-6567569	HUVEC	blood vessel:	n/a	chr9:6567215-6567222 chr9:6566672-6566682
2	NFIC	chr9:6566371-6566900	SK-N-SH	brain:	n/a	n/a
3	FOS	chr9:6566370-6567598	MCF10A-Er-Src	breast:	n/a	chr9:6567211-6567221 chr9:6566601-6566612 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
4	POLR2A	chr9:6566356-6566709	HUVEC	blood vessel:	n/a	n/a
5	EP300	chr9:6566113-6567841	SK-N-SH	brain:	n/a	chr9:6566309-6566323 chr9:6566308-6566322
6	GABPA	chr9:6566283-6566861	A549	lung:	n/a	n/a
7	PBX3	chr9:6566317-6567777	SK-N-SH	brain:	n/a	n/a
8	MXI1	chr9:6566385-6567534	Hela-S3	cervix:	n/a	n/a
9	GTF2F1	chr9:6566344-6567658	Hela-S3	cervix:	n/a	n/a
10	JUND	chr9:6566243-6567826	SK-N-SH	brain:	n/a	chr9:6567211-6567221 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
11	POLR2A	chr9:6565867-6567710	HUVEC	blood vessel:	n/a	n/a
12	JUND	chr9:6566221-6567828	SK-N-SH	brain:	n/a	chr9:6567211-6567221 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
13	POLR2A	chr9:6566359-6567837	IMR90	lung:	n/a	n/a
14	TCF12	chr9:6566144-6567850	SK-N-SH	brain:	n/a	chr9:6566490-6566498
15	POLR2A	chr9:6566254-6567809	U87	brain:	n/a	n/a
16	RXRA	chr9:6566251-6566945	SK-N-SH	brain:	n/a	chr9:6566688-6566697
17	STAT3	chr9:6566277-6567631	MCF10A-Er-Src	breast:	n/a	chr9:6567275-6567283
18	POLR2A	chr9:6566345-6566792	U87	brain:	n/a	n/a
19	SP1	chr9:6566298-6567723	A549	lung:	n/a	n/a
20	FOSL1	chr9:6566097-6567815	HCT-116	colon:	n/a	chr9:6567211-6567221 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
21	GATA3	chr9:6566211-6567833	SK-N-SH	brain:	n/a	chr9:6567733-6567740 chr9:6567215-6567222 chr9:6567733-6567740 chr9:6567726-6567747 chr9:6566672-6566682 chr9:6567733-6567740
22	TAF1	chr9:6566385-6566730	SK-N-SH	brain:	n/a	n/a
23	EP300	chr9:6566294-6567636	Hela-S3	cervix:	n/a	chr9:6566309-6566323 chr9:6566308-6566322
24	STAT3	chr9:6566280-6567631	MCF10A-Er-Src	breast:	n/a	chr9:6567275-6567283
25	POLR2A	chr9:6566355-6566751	Hela-S3	cervix:	n/a	n/a
26	RUNX3	chr9:6566390-6566813	GM12878	blood:	n/a	n/a
27	ELK4	chr9:6566118-6567064	Hela-S3	cervix:	n/a	n/a
28	TBP	chr9:6566281-6567732	Hela-S3	cervix:	n/a	n/a
29	GATA3	chr9:6566279-6567693	A549	lung:	n/a	chr9:6567215-6567222 chr9:6566672-6566682
30	MAX	chr9:6566351-6567611	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr9:6566254-6567803	U87	brain:	n/a	n/a
32	MAX	chr9:6566269-6566799	SK-N-SH	brain:	n/a	n/a
33	CEBPB	chr9:6566329-6566853	IMR90	lung:	n/a	n/a
34	MAX	chr9:6566204-6567693	A549	lung:	n/a	n/a
35	POLR2A	chr9:6566318-6567675	SK-N-SH	brain:	n/a	n/a
36	NFIC	chr9:6566323-6566895	GM12878	blood:	n/a	n/a
37	POLR2A	chr9:6566340-6566709	HCT-116	colon:	n/a	n/a
38	EP300	chr9:6566280-6566955	A549	lung:	n/a	chr9:6566309-6566323 chr9:6566308-6566322
39	JUND	chr9:6566173-6567762	Hela-S3	cervix:	n/a	chr9:6567211-6567221 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
40	CEBPB	chr9:6566241-6567786	HCT-116	colon:	n/a	n/a
41	PBX3	chr9:6566252-6567812	SK-N-SH	brain:	n/a	n/a
42	POLR2A	chr9:6566326-6566788	HCT-116	colon:	n/a	n/a
43	SP1	chr9:6566316-6566904	A549	lung:	n/a	n/a
44	GABPA	chr9:6566247-6566769	SK-N-SH	brain:	n/a	n/a
45	JUND	chr9:6566221-6567917	HCT-116	colon:	n/a	chr9:6567211-6567221 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
46	EP300	chr9:6566154-6567666	SK-N-SH	brain:	n/a	chr9:6566309-6566323 chr9:6566308-6566322
47	JUN	chr9:6566318-6567618	HUVEC	blood vessel:	n/a	chr9:6567211-6567221 chr9:6567182-6567193 chr9:6567211-6567221 chr9:6566627-6566637 chr9:6567332-6567341 chr9:6567182-6567192 chr9:6566627-6566637 chr9:6567183-6567191 chr9:6567211-6567221 chr9:6566629-6566640 chr9:6566626-6566638 chr9:6567182-6567192 chr9:6567211-6567221
48	FOSL2	chr9:6566367-6566825	A549	lung:	n/a	chr9:6566627-6566637 chr9:6566627-6566637 chr9:6566629-6566640 chr9:6566626-6566638
49	POLR2A	chr9:6566313-6567728	HUVEC	blood vessel:	n/a	n/a
50	POLR2A	chr9:6565947-6567850	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:6411889..6413422-chr9:6565833..6568598,2	K562	blood:

Variant related genes	Relation type
ENSG00000237158	TF binding region
GLDC	TF binding region
ENSG00000147854	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10975645	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs10975647	1.00[YRI][hapmap];0.95[AFR][1000 genomes]
rs12339196	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12349059	1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs28404672	0.94[AFR][1000 genomes]
rs9299033	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1031086	chr9:5806949-6630686	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv539967	chr9:5806949-6630686	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv933124	chr9:6099101-6644738	Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1029000	chr9:6188652-6687205	Enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
5	nsv1031459	chr9:6216913-6657192	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv948562	chr9:6222553-6684955	Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv1032350	chr9:6328167-6630686	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv831497	chr9:6377501-6612402	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
9	nsv892162	chr9:6480005-6788085	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
10	nsv831498	chr9:6496021-6689728	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
11	nsv934176	chr9:6517535-6644738	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv892163	chr9:6523056-6632061	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1025627	chr9:6523056-6648098	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
14	esv2752308	chr9:6523060-6899149	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
15	nsv613206	chr9:6525753-6686738	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
16	esv3324686	chr9:6528411-6728310	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
17	nsv1028402	chr9:6542253-6874231	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
18	nsv1018308	chr9:6544766-6869653	Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
19	nsv1015462	chr9:6544766-6874231	Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
20	nsv1018870	chr9:6548393-6708345	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
21	nsv892164	chr9:6555079-6664282	Enhancers Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
22	nsv931094	chr9:6558442-6672439	ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
23	nsv870402	chr9:6565246-7016784	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:6532000-6570400	Strong transcription	Liver	Liver
2	chr9:6554600-6568600	Weak transcription	Fetal Intestine Small	intestine
3	chr9:6556000-6566800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr9:6558600-6567000	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr9:6558600-6586600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr9:6558800-6580800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr9:6559200-6583400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr9:6559600-6568200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr9:6559800-6567600	Strong transcription	HUES6 Cell Line	embryonic stem cell
10	chr9:6560200-6569400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:6560200-6572200	Weak transcription	GM12878-XiMat	blood
12	chr9:6561200-6591000	Weak transcription	Placenta	Placenta
13	chr9:6561600-6566800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr9:6561600-6566800	Enhancers	HUVEC	blood vessel
15	chr9:6561800-6566800	Enhancers	Muscle Satellite Cultured Cells	--
16	chr9:6562800-6566800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
17	chr9:6563000-6566800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:6563000-6566800	Enhancers	Osteobl	bone
19	chr9:6563000-6567000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr9:6563000-6567400	Strong transcription	H9 Cell Line	embryonic stem cell
21	chr9:6563400-6566800	Weak transcription	Spleen	Spleen
22	chr9:6563400-6583000	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr9:6563600-6566600	Weak transcription	HSMMtube	muscle
24	chr9:6564200-6566600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr9:6564200-6566800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr9:6564200-6566800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr9:6564400-6566800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr9:6564400-6566800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr9:6564400-6566800	Enhancers	HMEC	breast
30	chr9:6564400-6566800	Enhancers	NHDF-Ad	bronchial
31	chr9:6564400-6567400	Strong transcription	HepG2	liver
32	chr9:6564400-6568000	Enhancers	Brain Hippocampus Middle	brain
33	chr9:6564600-6566600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr9:6564600-6566800	Enhancers	HSMM	muscle
35	chr9:6564600-6566800	Enhancers	NHEK	skin
36	chr9:6564600-6566800	Enhancers	NHLF	lung
37	chr9:6564600-6568000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr9:6564800-6568200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr9:6565000-6566800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr9:6565000-6566800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr9:6565200-6566800	Weak transcription	Right Atrium	heart
42	chr9:6565200-6566800	Enhancers	NH-A	brain
43	chr9:6565200-6567000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr9:6565200-6567000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr9:6565200-6567200	Weak transcription	Aorta	Aorta
46	chr9:6565400-6566600	Enhancers	A549	lung
47	chr9:6565400-6575200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr9:6565400-6586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr9:6565600-6567000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:6565600-6567200	Enhancers	Brain Inferior Temporal Lobe	brain

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