Variant report

Variant	rs12219637
Chromosome Location	chr10:27225904-27225905
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	chr10:27225900-27226050	GM12872	blood:	n/a	n/a
2	POLR2A	chr10:27225824-27225948	MCF-7	breast:	n/a	n/a

Variant related genes	Relation type
LINC00202-1	TF binding region

Extended variants
information (count: 137 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10829143	0.89[ASN][1000 genomes]
rs10829144	0.88[ASN][1000 genomes]
rs10829145	0.88[ASN][1000 genomes]
rs10829146	0.91[AMR][1000 genomes]
rs10829147	0.85[ASN][1000 genomes]
rs11015388	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11015389	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015392	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11015393	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015394	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11015397	0.90[ASN][1000 genomes]
rs11015398	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015408	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11015417	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015418	0.86[ASN][1000 genomes]
rs11015419	0.87[ASN][1000 genomes]
rs11015420	0.87[ASN][1000 genomes]
rs11015422	0.91[AMR][1000 genomes]
rs11015423	0.85[ASN][1000 genomes]
rs11015430	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015432	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015434	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11015449	1.00[YRI][hapmap]
rs12218581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12220671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12412861	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12413543	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12416077	1.00[YRI][hapmap]
rs12416080	1.00[YRI][hapmap]
rs12570065	1.00[YRI][hapmap]
rs12572726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12572741	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12573020	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12573785	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12774303	0.89[CEU][hapmap]
rs12775377	0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12779247	0.88[CEU][hapmap]
rs12779943	0.87[CEU][hapmap]
rs12783077	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1329993	1.00[YRI][hapmap]
rs2211443	0.85[ASN][1000 genomes]
rs28417098	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34163327	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34273816	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34319528	0.89[AMR][1000 genomes]
rs34364574	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34416280	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34479281	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34694994	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34974756	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35163810	0.89[AMR][1000 genomes]
rs35213008	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35606227	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35844030	0.88[CEU][hapmap]
rs35945396	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3737056	0.89[CEU][hapmap]
rs3781099	0.88[CEU][hapmap]
rs3781102	1.00[YRI][hapmap]
rs3818634	0.80[CEU][hapmap]
rs3928123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41279934	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41279936	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs41279938	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4306204	0.85[ASN][1000 genomes]
rs4747579	0.85[ASN][1000 genomes]
rs4749199	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4749200	0.98[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4749201	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4749203	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4749204	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4749205	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4749206	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4749207	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4749208	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4749209	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4749210	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4749222	1.00[YRI][hapmap]
rs58651764	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60658625	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66462820	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67387186	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs71483822	0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72629751	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7475282	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787430	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787434	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9787435	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9787668	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:49 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3415799	chr10:26929831-27233591	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831812	chr10:27061506-27234267	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757376	chr10:27160932-27229993	Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	esv2759740	chr10:27160932-27229993	Strong transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv430140	chr10:27165095-27227681	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	esv2752390	chr10:27165095-27241780	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv894978	chr10:27185286-27239820	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv1036080	chr10:27215829-27229993	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2753500	chr10:27221957-27231610	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv2754229	chr10:27222320-27228439	ZNF genes & repeats Weak transcription Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv2754956	chr10:27222320-27228439	Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv430141	chr10:27222320-27228439	Enhancers Weak transcription ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv2752676	chr10:27222320-27229993	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv512154	chr10:27222630-27227307	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
15	esv3528438	chr10:27223268-27228174	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	esv2752915	chr10:27223642-27228439	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
17	esv2755304	chr10:27223642-27228439	Weak transcription ZNF genes & repeats Enhancers Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	esv2755811	chr10:27223642-27228439	Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
19	esv2756660	chr10:27223642-27228439	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	esv2755698	chr10:27223642-27231610	Enhancers Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv2753825	chr10:27223642-27241780	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
22	esv2754238	chr10:27223642-27241780	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	esv3528441	chr10:27224050-27228175	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
24	esv3319062	chr10:27224066-27228216	ZNF genes & repeats Active TSS Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
25	esv3319051	chr10:27224115-27228174	ZNF genes & repeats Active TSS Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	esv3528439	chr10:27224144-27228137	Enhancers ZNF genes & repeats Weak transcription Active TSS	TF binding region	1 gene(s)	inside rSNPs	diseases
27	esv3417794	chr10:27224164-27228107	Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
28	esv3319040	chr10:27224186-27228091	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
29	esv3528437	chr10:27224194-27228096	Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
30	esv3319073	chr10:27224201-27228089	Weak transcription ZNF genes & repeats Active TSS Enhancers	TF binding region	1 gene(s)	inside rSNPs	diseases
31	esv3528442	chr10:27224201-27228089	Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region	1 gene(s)	inside rSNPs	diseases
32	nsv947784	chr10:27224620-27235850	Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
33	esv12865	chr10:27224672-27229578	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
34	nsv820780	chr10:27224672-27229578	Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
35	esv2750887	chr10:27225647-27228439	Enhancers Active TSS Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
36	esv2754977	chr10:27225647-27228439	Weak transcription Active TSS Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
37	esv2756680	chr10:27225647-27228439	Weak transcription Enhancers ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
38	nsv430142	chr10:27225647-27228439	Enhancers Weak transcription Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
39	esv2756477	chr10:27225647-27229993	ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
40	nsv430144	chr10:27225647-27230675	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
41	esv2750888	chr10:27225647-27241780	ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
42	esv2755394	chr10:27225904-27228439	Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
43	esv1797489	chr10:27225904-27228473	ZNF genes & repeats Enhancers Weak transcription Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
44	esv2760143	chr10:27225904-27228473	Enhancers Active TSS ZNF genes & repeats Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
45	esv2760211	chr10:27225904-27235834	Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
46	nsv1047111	chr10:27225904-27242991	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
47	nsv1036722	chr10:27225904-27243972	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
48	nsv1043456	chr10:27225904-27246821	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
49	nsv442174	chr10:27225905-27228473	Enhancers ZNF genes & repeats Active TSS Weak transcription	TF binding region Chromatin interactive region	1 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	chr10:27220600-27228000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr10:27220600-27234200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr10:27220800-27226400	Weak transcription	Fetal Muscle Leg	muscle
4	chr10:27220800-27235200	Weak transcription	Gastric	stomach
5	chr10:27225800-27226200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:27225800-27226600	Enhancers	Fetal Muscle Trunk	muscle

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