Variant report

Variant	rs10992476
Chromosome Location	chr9:95571272-95571273
allele	A/G
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	MAX	chr9:95570827-95571931	HCT-116	colon:	n/a	chr9:95571535-95571544 chr9:95571081-95571091 chr9:95571345-95571354
2	NFIC	chr9:95571019-95571589	ECC-1	luminal epithelium:	n/a	n/a
3	POLR2A	chr9:95571247-95571275	MCF-7	breast:	n/a	n/a
4	SUZ12	chr9:95571016-95571696	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr9:95570924-95571823	HCT-116	colon:	n/a	n/a
6	CTCF	chr9:95571160-95571310	A549	lung:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
7	CTCF	chr9:95571031-95571302	GM19238	blood:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
8	CTCF	chr9:95571057-95571325	NHEK	skin:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
9	MAX	chr9:95570853-95571875	HCT-116	colon:	n/a	chr9:95571535-95571544 chr9:95571081-95571091 chr9:95571345-95571354
10	CTCF	chr9:95570989-95571636	H1-hESC	embryonic stem cell:	n/a	chr9:95571189-95571197 chr9:95571520-95571538 chr9:95571179-95571195 chr9:95571522-95571535
11	POLR2A	chr9:95571034-95571351	A549	lung:	n/a	n/a
12	CTCF	chr9:95571062-95571314	GM19240	blood:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
13	KAP1	chr9:95571026-95571712	HEK293	kidney:	n/a	n/a
14	KAP1	chr9:95571131-95571645	U2OS	brain:	n/a	n/a
15	RAD21	chr9:95571044-95571302	HepG2	liver:	n/a	chr9:95571189-95571198
16	MAZ	chr9:95571211-95571810	IMR90	lung:	n/a	chr9:95571535-95571544 chr9:95571345-95571354
17	POLR2A	chr9:95571163-95571877	H1-neurons	neurons:	n/a	n/a
18	ELF1	chr9:95571185-95571822	GM12878	blood:	n/a	chr9:95571296-95571305
19	GABPA	chr9:95570928-95571738	MCF-7	breast:	n/a	chr9:95571497-95571511
20	TCF3	chr9:95571082-95571276	GM12878	blood:	n/a	n/a
21	BRCA1	chr9:95571272-95571377	H1-hESC	embryonic stem cell:	n/a	n/a
22	CTCF	chr9:95571160-95571310	MCF-7	breast:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
23	CTCF	chr9:95571058-95571336	MCF-7	breast:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
24	MXI1	chr9:95571270-95571944	IMR90	lung:	n/a	n/a
25	RCOR1	chr9:95571214-95571833	IMR90	lung:	n/a	n/a
26	ZNF263	chr9:95571066-95571766	HEK293-T-REx	kidney:	n/a	n/a
27	POLR2A	chr9:95571046-95571767	HCT-116	colon:	n/a	n/a
28	CTCF	chr9:95571101-95571282	Pancreas_OC	pancreas:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
29	CTCF	chr9:95571180-95571330	SK-N-SH_RA	brain:	n/a	chr9:95571189-95571197
30	CTCF	chr9:95571069-95571287	A549	lung:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
31	MAX	chr9:95570923-95571865	ECC-1	luminal epithelium:	n/a	chr9:95571535-95571544 chr9:95571081-95571091 chr9:95571345-95571354
32	YY1	chr9:95570956-95571636	HCT-116	colon:	n/a	chr9:95571296-95571310
33	GABPA	chr9:95570873-95571750	H1-hESC	embryonic stem cell:	n/a	chr9:95571497-95571511
34	CTCF	chr9:95571140-95571290	GM12864	blood:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
35	POLR2A	chr9:95571102-95571813	HEK293	kidney:	n/a	n/a
36	MAX	chr9:95570997-95571823	H1-hESC	embryonic stem cell:	n/a	chr9:95571535-95571544 chr9:95571081-95571091 chr9:95571345-95571354
37	RAD21	chr9:95570769-95571363	H1-hESC	embryonic stem cell:	n/a	chr9:95571189-95571198
38	CTCF	chr9:95571042-95571870	A549	lung:	n/a	chr9:95571189-95571197 chr9:95571520-95571538 chr9:95571179-95571195 chr9:95571522-95571535
39	CTCF	chr9:95571200-95571350	Caco-2	colon:	n/a	n/a
40	CTCF	chr9:95571057-95571327	GM12892	blood:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
41	MAX	chr9:95571026-95571459	MCF-7	breast:	n/a	chr9:95571081-95571091 chr9:95571345-95571354
42	E2F6	chr9:95570911-95571828	H1-hESC	embryonic stem cell:	n/a	chr9:95570983-95570993 chr9:95571300-95571310 chr9:95571161-95571172 chr9:95571501-95571510 chr9:95571085-95571095 chr9:95571297-95571307
43	GABPA	chr9:95570745-95571788	H1-hESC	embryonic stem cell:	n/a	chr9:95571497-95571511
44	GABPA	chr9:95570939-95571824	MCF-7	breast:	n/a	chr9:95571497-95571511
45	ZNF143	chr9:95570912-95571581	H1-hESC	embryonic stem cell:	n/a	chr9:95571085-95571095
46	CTCF	chr9:95570976-95571301	H1-hESC	embryonic stem cell:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
47	SUZ12	chr9:95569398-95572352	NT2-D1	testis:	n/a	n/a
48	TAF1	chr9:95571016-95571804	H1-hESC	embryonic stem cell:	n/a	n/a
49	CTCF	chr9:95571140-95571290	HRE	kidney:	n/a	chr9:95571189-95571197 chr9:95571179-95571195
50	CTCF	chr9:95571026-95571634	GM12878	blood:	n/a	chr9:95571189-95571197 chr9:95571520-95571538 chr9:95571179-95571195 chr9:95571522-95571535

No.	Distal block	Cell Line	Cell type
1	chr9:95570373..95571952-chr9:95637590..95640500,2	MCF-7	breast:
2	chr9:95570706..95571359-chr9:95719247..95719879,2	MCF-7	breast:
3	chr9:95431331..95434473-chr9:95569877..95572688,3	MCF-7	breast:

Variant related genes	Relation type
ANKRD19P	TF binding region
ENSG00000127081	Chromatin interaction
ENSG00000127080	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10821001	0.87[EUR][1000 genomes]
rs10821003	0.87[EUR][1000 genomes]
rs10821004	0.88[EUR][1000 genomes]
rs10821005	0.88[EUR][1000 genomes]
rs10821011	0.88[EUR][1000 genomes]
rs10821014	0.88[EUR][1000 genomes]
rs10992396	0.85[EUR][1000 genomes]
rs10992407	0.85[EUR][1000 genomes]
rs10992408	0.85[EUR][1000 genomes]
rs10992409	0.85[EUR][1000 genomes]
rs10992412	0.85[EUR][1000 genomes]
rs10992414	0.86[EUR][1000 genomes]
rs10992416	0.86[EUR][1000 genomes]
rs10992417	0.86[EUR][1000 genomes]
rs10992420	0.87[EUR][1000 genomes]
rs10992422	0.88[EUR][1000 genomes]
rs10992423	0.87[EUR][1000 genomes]
rs10992437	0.87[EUR][1000 genomes]
rs10992448	0.88[EUR][1000 genomes]
rs10992453	0.88[EUR][1000 genomes]
rs10992460	0.90[EUR][1000 genomes]
rs10992461	0.90[EUR][1000 genomes]
rs10992474	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10992475	0.90[ASN][1000 genomes]
rs11533010	0.88[EUR][1000 genomes]
rs12057034	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12236754	0.88[EUR][1000 genomes]
rs12238691	0.88[EUR][1000 genomes]
rs12684076	0.84[EUR][1000 genomes]
rs12684587	0.87[EUR][1000 genomes]
rs12685358	0.88[EUR][1000 genomes]
rs16908555	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs16908560	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1853427	0.89[ASN][1000 genomes]
rs1853428	0.83[EUR][1000 genomes]
rs1853429	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1974004	0.83[EUR][1000 genomes]
rs2181584	0.88[EUR][1000 genomes]
rs2398780	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3739605	0.88[EUR][1000 genomes]
rs4141966	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56311406	0.90[EUR][1000 genomes]
rs57737182	0.90[EUR][1000 genomes]
rs58952648	0.88[EUR][1000 genomes]
rs60498616	0.88[EUR][1000 genomes]
rs7031163	0.88[EUR][1000 genomes]
rs72618187	0.86[ASN][1000 genomes]
rs753804	0.88[EUR][1000 genomes]
rs754600	0.82[EUR][1000 genomes]
rs7850075	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7855203	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7859967	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7860628	0.90[EUR][1000 genomes]
rs7863741	0.91[EUR][1000 genomes]
rs7869603	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831654	chr9:95542920-95720961	ZNF genes & repeats Flanking Active TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv972420	chr9:95566045-95588965	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	esv3373736	chr9:95569656-95572504	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:95569400-95571400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
2	chr9:95569400-95571600	Bivalent Enhancer	Fetal Muscle Leg	muscle
3	chr9:95569400-95572400	Bivalent Enhancer	Fetal Brain Male	brain
4	chr9:95569400-95572400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr9:95569400-95572400	Bivalent Enhancer	Fetal Thymus	thymus
6	chr9:95569600-95571400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
7	chr9:95569600-95572200	Bivalent Enhancer	Fetal Stomach	stomach
8	chr9:95569600-95572400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr9:95569600-95572400	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
10	chr9:95569600-95572400	Flanking Bivalent TSS/Enh	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr9:95569600-95572400	Flanking Active TSS	Right Ventricle	heart
12	chr9:95569600-95572600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr9:95569800-95571600	Bivalent Enhancer	Placenta	Placenta
14	chr9:95569800-95572200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr9:95569800-95572400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr9:95569800-95572400	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
17	chr9:95570000-95571800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
18	chr9:95570000-95571800	Bivalent/Poised TSS	Colon Smooth Muscle	Colon
19	chr9:95570000-95571800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
20	chr9:95570000-95572000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
21	chr9:95570000-95572200	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:95570000-95572400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
23	chr9:95570000-95572400	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
24	chr9:95570000-95572400	Bivalent Enhancer	Liver	Liver
25	chr9:95570000-95572600	Bivalent Enhancer	Stomach Mucosa	stomach
26	chr9:95570200-95571600	Bivalent/Poised TSS	A549	lung
27	chr9:95570200-95572000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr9:95570200-95572400	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
29	chr9:95570200-95572400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
30	chr9:95570400-95571400	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
31	chr9:95570400-95571800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr9:95570400-95571800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
33	chr9:95570400-95571800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr9:95570400-95571800	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr9:95570400-95572000	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
36	chr9:95570400-95572200	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr9:95570400-95572400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
38	chr9:95570400-95572400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr9:95570400-95572400	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
40	chr9:95570600-95571400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
41	chr9:95570600-95571400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
42	chr9:95570600-95571400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr9:95570600-95571400	Flanking Bivalent TSS/Enh	Brain Inferior Temporal Lobe	brain
44	chr9:95570600-95571400	Bivalent Enhancer	GM12878-XiMat	blood
45	chr9:95570600-95571600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr9:95570600-95571800	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
47	chr9:95570600-95571800	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
48	chr9:95570600-95571800	Flanking Bivalent TSS/Enh	HMEC	breast
49	chr9:95570600-95572200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
50	chr9:95570600-95572200	Bivalent/Poised TSS	Thymus	Thymus

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