Variant report

Variant	rs12243621
Chromosome Location	chr10:90657317-90657318
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	BRCA1	chr10:90657229-90657818	Hela-S3	cervix:	n/a	n/a
2	CEBPB	chr10:90656686-90657807	HCT-116	colon:	n/a	n/a
3	EP300	chr10:90656674-90657686	SK-N-SH	brain:	n/a	chr10:90657116-90657129
4	CEBPB	chr10:90657035-90657474	Hela-S3	cervix:	n/a	n/a
5	EP300	chr10:90656897-90657517	SK-N-SH_RA	brain:	n/a	chr10:90657116-90657129
6	USF2	chr10:90656876-90657617	Hela-S3	cervix:	n/a	n/a
7	MXI1	chr10:90657086-90657366	Hela-S3	cervix:	n/a	n/a
8	GATA3	chr10:90657021-90657592	MCF-7	breast:	n/a	n/a
9	FOSL1	chr10:90656833-90657740	HCT-116	colon:	n/a	n/a
10	KAP1	chr10:90656033-90657749	U2OS	brain:	n/a	n/a
11	FOSL2	chr10:90656906-90657680	SK-N-SH	brain:	n/a	n/a
12	TEAD4	chr10:90656937-90657674	SK-N-SH	brain:	n/a	n/a
13	PBX3	chr10:90656812-90657646	SK-N-SH	brain:	n/a	n/a
14	KAP1	chr10:90656110-90657745	HEK293	kidney:	n/a	n/a
15	TCF7L2	chr10:90656850-90657788	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr10:90656720-90657581	SK-N-SH	brain:	n/a	n/a
17	EP300	chr10:90657148-90657565	Hela-S3	cervix:	n/a	n/a
18	GATA3	chr10:90656666-90657927	SK-N-SH	brain:	n/a	n/a
19	PBX3	chr10:90656847-90657695	SK-N-SH	brain:	n/a	n/a
20	TCF12	chr10:90656631-90657739	SK-N-SH	brain:	n/a	n/a
21	NFIC	chr10:90656923-90657698	SK-N-SH	brain:	n/a	n/a
22	RAD21	chr10:90657201-90657461	Hela-S3	cervix:	n/a	n/a
23	POLR2A	chr10:90657146-90657520	HCT-116	colon:	n/a	n/a
24	RCOR1	chr10:90656980-90657429	Hela-S3	cervix:	n/a	n/a
25	TCF7L2	chr10:90657044-90657577	HEK293	kidney:	n/a	n/a
26	STAT1	chr10:90656033-90657545	Hela-S3	cervix:	n/a	chr10:90656641-90656652 chr10:90656268-90656279 chr10:90656270-90656279 chr10:90656269-90656278
27	POLR2A	chr10:90656107-90658222	GM12891	blood:	n/a	n/a
28	GATA3	chr10:90656712-90657815	SK-N-SH	brain:	n/a	n/a
29	SMC3	chr10:90656946-90657563	Hela-S3	cervix:	n/a	n/a
30	JUND	chr10:90656802-90657631	HCT-116	colon:	n/a	n/a
31	GTF2F1	chr10:90656793-90657526	Hela-S3	cervix:	n/a	n/a
32	MAX	chr10:90656854-90657560	Hela-S3	cervix:	n/a	n/a
33	TCF12	chr10:90656774-90657768	SK-N-SH	brain:	n/a	n/a
34	RFX5	chr10:90657016-90657526	Hela-S3	cervix:	n/a	n/a
35	RXRA	chr10:90656942-90657614	SK-N-SH	brain:	n/a	chr10:90657321-90657335
36	MAX	chr10:90656867-90657547	Hela-S3	cervix:	n/a	n/a
37	TCF7L2	chr10:90656838-90657590	Hela-S3	cervix:	n/a	n/a
38	SP1	chr10:90655989-90657715	HCT-116	colon:	n/a	chr10:90657194-90657201 chr10:90656309-90656330
39	NR2F2	chr10:90657121-90657559	MCF-7	breast:	n/a	chr10:90657136-90657151
40	POLR2A	chr10:90656806-90657590	Hela-S3	cervix:	n/a	n/a
41	GATA3	chr10:90656893-90657758	A549	lung:	n/a	n/a
42	TCF7L2	chr10:90656935-90657615	HCT-116	colon:	n/a	n/a
43	EP300	chr10:90657006-90657484	SK-N-SH_RA	brain:	n/a	chr10:90657116-90657129

Variant related genes	Relation type
STAMBPL1	TF binding region

Extended variants
information (count: 85 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1029024	0.82[CHB][hapmap]
rs10509555	1.00[EUR][1000 genomes]
rs10509556	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs10509558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509559	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10509560	0.91[CHB][hapmap]
rs11202885	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11202906	0.91[CHB][hapmap]
rs11202907	0.91[CHB][hapmap]
rs12240659	0.90[AFR][1000 genomes]
rs12242274	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12243282	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12245057	0.98[AFR][1000 genomes]
rs12245122	0.98[AFR][1000 genomes]
rs12245525	1.00[EUR][1000 genomes]
rs12245668	1.00[EUR][1000 genomes]
rs12247227	0.88[CHB][hapmap];0.86[ASN][1000 genomes]
rs12254451	1.00[EUR][1000 genomes]
rs12257540	1.00[EUR][1000 genomes]
rs12258025	0.98[AFR][1000 genomes]
rs12260572	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12261664	0.86[ASN][1000 genomes]
rs12262461	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12263461	1.00[EUR][1000 genomes]
rs12264840	0.91[CHB][hapmap]
rs12266993	0.98[AFR][1000 genomes]
rs12413277	1.00[EUR][1000 genomes]
rs12414800	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113311	1.00[EUR][1000 genomes]
rs17113344	1.00[EUR][1000 genomes]
rs17113363	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113426	1.00[EUR][1000 genomes]
rs17113457	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113476	0.83[CHB][hapmap];1.00[EUR][1000 genomes]
rs17113724	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113942	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17113959	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114016	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114020	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114057	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17114116	0.91[CHB][hapmap]
rs17114143	0.91[CHB][hapmap]
rs17114186	0.91[CHB][hapmap]
rs17114283	0.91[CHB][hapmap]
rs2119685	0.91[CHB][hapmap]
rs2231780	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231785	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231786	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282122	1.00[EUR][1000 genomes]
rs35996190	1.00[EUR][1000 genomes]
rs3781206	0.91[CHB][hapmap]
rs3781208	0.91[CHB][hapmap]
rs3814691	0.82[CHB][hapmap];1.00[EUR][1000 genomes]
rs3816245	0.91[CHB][hapmap]
rs3898173	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3898174	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56998609	1.00[EUR][1000 genomes]
rs58673564	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58986570	1.00[EUR][1000 genomes]
rs59661152	1.00[EUR][1000 genomes]
rs60349051	1.00[EUR][1000 genomes]
rs60523093	1.00[EUR][1000 genomes]
rs7070713	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs7077019	1.00[EUR][1000 genomes]
rs7078383	0.91[CHB][hapmap]
rs7085698	0.91[CHB][hapmap]
rs7090604	1.00[EUR][1000 genomes]
rs7090631	0.91[CHB][hapmap]
rs7098235	0.91[CHB][hapmap]
rs7098246	1.00[EUR][1000 genomes]
rs73364839	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73364851	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74150103	0.86[ASN][1000 genomes]
rs7897521	0.91[CHB][hapmap]
rs7908852	0.91[CHB][hapmap]
rs7913997	1.00[EUR][1000 genomes]
rs7915393	0.91[CHB][hapmap]
rs9804254	0.98[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529324	chr10:90198865-90738588	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1042848	chr10:90466032-91318474	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv540741	chr10:90466032-91318474	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv831942	chr10:90564697-90730352	Flanking Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:100 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:90641400-90658600	Weak transcription	Brain Angular Gyrus	brain
2	chr10:90641800-90661800	Weak transcription	Thymus	Thymus
3	chr10:90642000-90684800	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr10:90642000-90686400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:90647400-90675200	Weak transcription	Spleen	Spleen
6	chr10:90647400-90681000	Weak transcription	Aorta	Aorta
7	chr10:90652000-90658200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr10:90652400-90663000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:90652600-90660800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr10:90652600-90661400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:90652800-90661200	Weak transcription	NHEK	skin
12	chr10:90652800-90661800	Weak transcription	HMEC	breast
13	chr10:90653600-90657600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr10:90653600-90659200	Enhancers	Fetal Intestine Small	intestine
15	chr10:90654000-90687400	Weak transcription	Right Ventricle	heart
16	chr10:90654200-90661800	Enhancers	Fetal Intestine Large	intestine
17	chr10:90654600-90657600	Enhancers	Liver	Liver
18	chr10:90654600-90658800	Weak transcription	Primary B cells from cord blood	blood
19	chr10:90654800-90657400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr10:90655000-90659000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr10:90655200-90675200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:90655200-90701400	Weak transcription	Gastric	stomach
23	chr10:90655400-90657400	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr10:90655400-90657600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr10:90655400-90658800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr10:90655400-90661200	Weak transcription	Fetal Thymus	thymus
27	chr10:90655800-90657600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr10:90655800-90658000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr10:90655800-90658600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr10:90655800-90658800	Enhancers	Primary T helper cells fromperipheralblood	blood
31	chr10:90655800-90660600	Weak transcription	Dnd41	blood
32	chr10:90656000-90657400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr10:90656000-90657600	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr10:90656000-90657600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr10:90656000-90657600	Enhancers	Brain Hippocampus Middle	brain
36	chr10:90656000-90657800	Enhancers	Muscle Satellite Cultured Cells	--
37	chr10:90656000-90658000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
38	chr10:90656000-90658000	Enhancers	Fetal Lung	lung
39	chr10:90656000-90658000	Enhancers	Stomach Mucosa	stomach
40	chr10:90656200-90657400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr10:90656200-90657400	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr10:90656200-90657600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr10:90656200-90657600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr10:90656200-90657600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr10:90656200-90657600	Enhancers	Colon Smooth Muscle	Colon
46	chr10:90656200-90657600	Enhancers	Fetal Muscle Leg	muscle
47	chr10:90656200-90657600	Enhancers	Placenta	Placenta
48	chr10:90656200-90657600	Enhancers	Ovary	ovary
49	chr10:90656200-90657600	Enhancers	Rectal Smooth Muscle	rectum
50	chr10:90656200-90657600	Enhancers	Right Atrium	heart

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