Variant report

Variant	rs7608938
Chromosome Location	chr2:99782226-99782227
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99782081..99783933-chr2:99796251..99798487,2	K562	blood:
2	chr2:99771110..99773673-chr2:99781018..99782915,3	MCF-7	breast:
3	chr2:99779845..99783199-chr2:99784390..99787805,3	K562	blood:

Variant related genes	Relation type
ENSG00000144182	Chromatin interaction
ENSG00000241962	Chromatin interaction
ENSG00000273155	Chromatin interaction
ENSG00000185414	Chromatin interaction
ENSG00000135951	Chromatin interaction
ENSG00000158411	Chromatin interaction

Extended variants
information (count: 165 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:161)

rs_ID	r²[population]
rs10167390	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10170063	0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10181422	0.81[ASN][1000 genomes]
rs1044575	0.87[EUR][1000 genomes]
rs10496334	0.94[CHB][hapmap]
rs10496335	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs10865029	0.84[EUR][1000 genomes]
rs11123761	0.83[EUR][1000 genomes]
rs11123762	0.84[EUR][1000 genomes]
rs11123763	0.84[EUR][1000 genomes]
rs11123764	0.84[EUR][1000 genomes]
rs11123765	0.92[EUR][1000 genomes]
rs11123766	0.85[EUR][1000 genomes]
rs11123770	0.97[EUR][1000 genomes]
rs1115756	0.86[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1115757	0.88[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1133977	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1133978	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11674894	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11677247	0.86[EUR][1000 genomes]
rs11677321	0.82[EUR][1000 genomes]
rs11678456	0.83[EUR][1000 genomes]
rs11683107	0.80[CHB][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11683188	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11685759	0.91[EUR][1000 genomes]
rs11688004	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11689265	0.93[EUR][1000 genomes]
rs11692336	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11692669	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11692699	0.84[EUR][1000 genomes]
rs11693427	0.84[EUR][1000 genomes]
rs11695379	0.84[EUR][1000 genomes]
rs11695751	0.88[EUR][1000 genomes]
rs11883676	0.87[EUR][1000 genomes]
rs11890338	0.86[EUR][1000 genomes]
rs11895749	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11900670	0.84[EUR][1000 genomes]
rs11903311	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12470471	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12613624	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12619780	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12620997	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs12621007	0.93[EUR][1000 genomes]
rs12987548	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12991189	0.93[EUR][1000 genomes]
rs12992218	0.86[EUR][1000 genomes]
rs12992930	0.87[EUR][1000 genomes]
rs12995473	0.86[EUR][1000 genomes]
rs12999417	0.84[EUR][1000 genomes]
rs13000731	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13004491	0.81[EUR][1000 genomes]
rs13008171	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13009147	0.86[EUR][1000 genomes]
rs13012481	0.84[EUR][1000 genomes]
rs13018891	0.86[EUR][1000 genomes]
rs13022329	0.84[EUR][1000 genomes]
rs13023501	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13023744	0.89[EUR][1000 genomes]
rs13026928	0.87[EUR][1000 genomes]
rs13030961	0.92[EUR][1000 genomes]
rs13031919	0.91[EUR][1000 genomes]
rs13033012	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13035311	0.83[EUR][1000 genomes]
rs13035357	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407840	0.83[ASN][1000 genomes]
rs13798	0.87[EUR][1000 genomes]
rs1453563	0.80[CHB][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1453564	0.82[ASN][1000 genomes]
rs1563106	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1563107	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1563108	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17020569	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17022180	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs17022249	0.94[CHB][hapmap];0.85[JPT][hapmap]
rs17708262	0.80[CHB][hapmap];0.91[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs17759607	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2084988	0.83[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2123686	0.80[CHB][hapmap]
rs2171359	0.87[EUR][1000 genomes]
rs2277876	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs2309581	0.87[EUR][1000 genomes]
rs2516827	0.86[EUR][1000 genomes]
rs2516828	0.86[EUR][1000 genomes]
rs2516829	0.86[EUR][1000 genomes]
rs2516830	0.80[CHB][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516832	0.86[EUR][1000 genomes]
rs2516833	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2516834	0.89[EUR][1000 genomes]
rs2516835	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516836	0.84[EUR][1000 genomes]
rs2632260	0.92[EUR][1000 genomes]
rs2632261	0.86[EUR][1000 genomes]
rs2632277	0.92[EUR][1000 genomes]
rs2632283	0.80[CHB][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632284	0.89[EUR][1000 genomes]
rs28648058	0.91[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2964969	0.87[EUR][1000 genomes]
rs2969379	0.92[EUR][1000 genomes]
rs34252185	0.89[EUR][1000 genomes]
rs34272114	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34766932	0.82[EUR][1000 genomes]
rs36071868	0.89[EUR][1000 genomes]
rs3762472	0.94[CHB][hapmap];0.87[JPT][hapmap]
rs3791211	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4340581	0.88[EUR][1000 genomes]
rs4347885	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4374423	0.80[CHB][hapmap]
rs4402818	0.83[EUR][1000 genomes]
rs4588238	0.83[EUR][1000 genomes]
rs4850895	0.94[CHB][hapmap];0.86[JPT][hapmap]
rs4850897	0.80[CHB][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4851183	0.80[CHB][hapmap];0.85[ASN][1000 genomes]
rs4851187	0.88[EUR][1000 genomes]
rs4851188	0.80[CHB][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62154638	0.88[ASN][1000 genomes]
rs6542846	0.82[ASN][1000 genomes]
rs6542863	0.84[EUR][1000 genomes]
rs6542864	0.84[EUR][1000 genomes]
rs6542865	0.86[EUR][1000 genomes]
rs6542866	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542868	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542869	0.87[EUR][1000 genomes]
rs6542870	0.87[EUR][1000 genomes]
rs6707462	0.83[ASN][1000 genomes]
rs6708576	0.87[EUR][1000 genomes]
rs6708878	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6712704	0.84[EUR][1000 genomes]
rs6717723	0.91[EUR][1000 genomes]
rs6717729	0.85[EUR][1000 genomes]
rs6722164	0.81[ASN][1000 genomes]
rs6724476	0.85[ASN][1000 genomes]
rs6727749	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6735801	0.80[CHB][hapmap];0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6737257	0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6739579	0.84[EUR][1000 genomes]
rs6740054	0.83[ASN][1000 genomes]
rs6743355	0.84[EUR][1000 genomes]
rs6750876	0.80[CHB][hapmap]
rs6751927	0.89[EUR][1000 genomes]
rs6753063	0.87[EUR][1000 genomes]
rs6753650	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754843	0.87[JPT][hapmap];0.87[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6756650	0.87[EUR][1000 genomes]
rs6757661	0.87[EUR][1000 genomes]
rs720228	0.88[EUR][1000 genomes]
rs720229	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7349217	0.85[EUR][1000 genomes]
rs7558004	0.87[EUR][1000 genomes]
rs7570657	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7571390	0.85[ASN][1000 genomes]
rs7572660	0.87[EUR][1000 genomes]
rs7577477	0.84[EUR][1000 genomes]
rs7584809	0.84[EUR][1000 genomes]
rs7586608	0.81[ASN][1000 genomes]
rs7591794	0.83[ASN][1000 genomes]
rs7604557	0.89[EUR][1000 genomes]
rs7605734	0.80[CHB][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7605843	0.87[EUR][1000 genomes]
rs7606635	0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs8179690	0.87[EUR][1000 genomes]
rs9941561	0.86[EUR][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv961842	chr2:99781138-99886836	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7608938	TSGA10	cis	lung	GTEx
rs7608938	TSGA10	cis	multi-tissue	Pritchard
rs7608938	TSGA10	cis	Whole Blood	GTEx
rs7608938	TSGA10	cis	Thyroid	GTEx
rs7608938	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs7608938	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs7608938	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs7608938	TSGA10	cis	Esophagus Mucosa	GTEx
rs7608938	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772200-99795600	Weak transcription	Gastric	stomach
2	chr2:99772400-99782800	Weak transcription	Aorta	Aorta
3	chr2:99772400-99784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:99772400-99784000	Weak transcription	Lung	lung
5	chr2:99772400-99784000	Weak transcription	Spleen	Spleen
6	chr2:99772400-99784800	Weak transcription	Pancreas	Pancrea
7	chr2:99772400-99786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:99772400-99786200	Weak transcription	Psoas Muscle	Psoas
9	chr2:99772400-99795600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:99772400-99795600	Weak transcription	Small Intestine	intestine
11	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
13	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
14	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr2:99772600-99783600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:99772600-99783600	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:99772600-99784000	Weak transcription	Thymus	Thymus
18	chr2:99772600-99784200	Weak transcription	HSMMtube	muscle
19	chr2:99772600-99784400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:99772600-99784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr2:99772600-99784800	Weak transcription	NH-A	brain
22	chr2:99772600-99786200	Weak transcription	NHLF	lung
23	chr2:99772600-99795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:99772600-99796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr2:99772600-99796600	Weak transcription	Fetal Kidney	kidney
26	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr2:99772800-99782600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr2:99772800-99783800	Weak transcription	HMEC	breast
29	chr2:99772800-99784000	Weak transcription	A549	lung
30	chr2:99772800-99786000	Weak transcription	Hela-S3	cervix
31	chr2:99772800-99796400	Weak transcription	Fetal Heart	heart
32	chr2:99773000-99796400	Weak transcription	Fetal Brain Male	brain
33	chr2:99773200-99790800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr2:99773600-99783000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
35	chr2:99773600-99785000	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr2:99773600-99790400	Strong transcription	Monocytes-CD14+_RO01746	blood
37	chr2:99773800-99784000	Weak transcription	HSMM	muscle
38	chr2:99774000-99784000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr2:99774000-99796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr2:99774200-99786000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr2:99774600-99795400	Weak transcription	K562	blood
42	chr2:99774800-99784800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr2:99775000-99795600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:99775200-99788600	Weak transcription	Fetal Intestine Small	intestine
45	chr2:99775200-99790400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr2:99775400-99783600	Weak transcription	Colon Smooth Muscle	Colon
47	chr2:99775400-99795400	Weak transcription	Brain Substantia Nigra	brain
48	chr2:99775800-99790400	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr2:99776400-99782600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr2:99776400-99784000	Weak transcription	Esophagus	oesophagus

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