Variant report

Variant	rs10494295
Chromosome Location	chr1:153195590-153195591
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	CTCF	chr1:153195540-153195690	BE2_C	brain:	n/a	n/a
2	CTCF	chr1:153195560-153195710	HUVEC	blood vessel:	n/a	n/a
3	CTCF	chr1:153195494-153195801	H1-hESC	embryonic stem cell:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
4	CTCF	chr1:153195580-153195730	GM12869	blood:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
5	RAD21	chr1:153195481-153195890	H1-hESC	embryonic stem cell:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
6	CTCF	chr1:153195560-153195710	HA-sp	spinal cord:	n/a	n/a
7	CTCF	chr1:153195466-153195970	A549	lung:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
8	CTCF	chr1:153195576-153195892	LNCaP	prostate:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
9	RAD21	chr1:153195484-153195884	H1-hESC	embryonic stem cell:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
10	CTCF	chr1:153195556-153195894	GM12892	blood:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
11	CTCF	chr1:153195588-153195867	GM13977	blood:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
12	CTCF	chr1:153195540-153195690	HVMF	connective:	n/a	n/a
13	RAD21	chr1:153195477-153195834	A549	lung:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
14	RAD21	chr1:153195495-153195836	ECC-1	luminal epithelium:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
15	CTCF	chr1:153195560-153195710	HPAF	blood vessel:	n/a	n/a
16	EBF1	chr1:153195568-153195764	GM12878	blood:	n/a	n/a
17	CTCF	chr1:153195560-153195710	HEEpiC	esophagus:	n/a	n/a
18	CTCF	chr1:153195540-153195690	GM06990	blood:	n/a	n/a
19	YY1	chr1:153195522-153195864	GM12878	blood:	n/a	chr1:153195780-153195788
20	CTCF	chr1:153195560-153195710	HBMEC	blood vessel:	n/a	n/a
21	CTCF	chr1:153195560-153195710	GM12868	blood:	n/a	n/a
22	RAD21	chr1:153195404-153195905	HCT-116	colon:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
23	CTCF	chr1:153195560-153195710	HAc	cerebellar:	n/a	n/a
24	CTCF	chr1:153195560-153195710	AG09309	skin:	n/a	n/a
25	SMC3	chr1:153195484-153195914	SK-N-SH	brain:	n/a	chr1:153195714-153195728
26	RAD21	chr1:153195427-153195847	ECC-1	luminal epithelium:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
27	CTCF	chr1:153195580-153195730	GM12864	blood:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
28	CTCF	chr1:153195560-153195710	HFF-Myc	foreskin:	n/a	n/a
29	RAD21	chr1:153195513-153195884	GM12878	blood:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
30	CTCF	chr1:153195560-153195710	GM12873	blood:	n/a	n/a
31	RAD21	chr1:153195521-153195863	GM12878	blood:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
32	CTCF	chr1:153195560-153195710	HRPEpiC	eye:	n/a	n/a
33	CTCF	chr1:153195560-153195710	NHDF-neo	bronchial:	n/a	n/a
34	CTCF	chr1:153195560-153195710	HL-60	blood:	n/a	n/a
35	CTCF	chr1:153195540-153195690	HCM	heart:	n/a	n/a
36	RAD21	chr1:153195475-153195806	SK-N-SH_RA	brain:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
37	CTCF	chr1:153195552-153195912	K562	blood:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
38	CTCF	chr1:153195560-153195710	GM12801	blood:	n/a	n/a
39	CTCF	chr1:153195580-153195730	HVMF	connective:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
40	CTCF	chr1:153195540-153195690	AG04450	lung:	n/a	n/a
41	SMC3	chr1:153195580-153195885	GM12878	blood:	n/a	chr1:153195714-153195728
42	CTCF	chr1:153195560-153195710	K562	blood:	n/a	n/a
43	CTCF	chr1:153195548-153195912	GM19238	blood:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
44	RAD21	chr1:153195492-153195839	MCF-7	breast:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
45	CTCF	chr1:153195560-153195710	GM12869	blood:	n/a	n/a
46	CTCF	chr1:153195590-153195879	ProgFib	skin:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
47	CTCF	chr1:153195580-153195807	HepG2	liver:	n/a	chr1:153195707-153195728 chr1:153195713-153195729 chr1:153195719-153195727 chr1:153195712-153195730 chr1:153195714-153195727
48	CTCF	chr1:153195540-153195690	GM12870	blood:	n/a	n/a
49	RAD21	chr1:153195482-153195888	A549	lung:	n/a	chr1:153195710-153195729 chr1:153195719-153195728 chr1:153195714-153195728
50	CTCF	chr1:153195560-153195710	HFF	foreskin:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:152890154..152890898-chr1:153195415..153196086,2	K562	blood:
2	chr1:152842274..152842902-chr1:153195531..153196166,2	K562	blood:
3	chr1:153162642..153163332-chr1:153195160..153195963,2	MCF-7	breast:
4	chr1:153188340..153191053-chr1:153194176..153196753,2	MCF-7	breast:
5	chr1:152843546..152844095-chr1:153194993..153195802,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000230779	TF binding region
ENSG00000203783	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10159119	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10494291	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10494292	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10494293	1.00[CEU][hapmap];0.90[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10494294	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10494296	0.82[EUR][1000 genomes]
rs10494297	0.84[EUR][1000 genomes]
rs10788862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10888536	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888537	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888538	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10888539	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205219	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11205222	1.00[CEU][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11205223	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11205225	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205227	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205228	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205229	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205230	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205231	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11205232	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11205238	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11205248	0.85[EUR][1000 genomes]
rs11583156	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11583609	0.84[EUR][1000 genomes]
rs11589914	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs12043009	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs12058098	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12062833	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12069007	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12122588	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12127862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12134915	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12136409	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142970	0.84[EUR][1000 genomes]
rs12740666	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12747804	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12755266	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12760683	0.81[EUR][1000 genomes]
rs1329094	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1329099	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1329100	0.99[EUR][1000 genomes]
rs1410859	1.00[CEU][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16835073	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16835081	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16835083	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16835093	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34119886	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35287517	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35358388	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs71626758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7538295	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013433	chr1:152619305-153262215	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
2	nsv535170	chr1:152619305-153262215	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv1001834	chr1:152648853-153279143	Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
4	nsv547899	chr1:152672005-153245082	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
5	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
6	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
7	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
8	nsv1004168	chr1:153088209-153226033	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
9	nsv1013041	chr1:153105260-153223716	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153183200-153205000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr1:153192800-153196600	Enhancers	Ovary	ovary
3	chr1:153195200-153195600	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:153195200-153195600	Enhancers	Esophagus	oesophagus
5	chr1:153195200-153195800	Enhancers	Brain Substantia Nigra	brain
6	chr1:153195400-153195600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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