Variant report

Variant	rs2969379
Chromosome Location	chr2:99776686-99776687
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:99767297..99778137-chr2:99793643..99800044,16	MCF-7	breast:
2	chr2:99770248..99774846-chr2:99775390..99781940,16	K562	blood:
3	chr2:99774991..99777436-chr2:99797785..99799967,2	MCF-7	breast:

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

Extended variants
information (count: 154 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:151)

rs_ID	r²[population]
rs10165534	0.85[ASN][1000 genomes]
rs10179043	0.87[ASN][1000 genomes]
rs10196680	0.85[ASN][1000 genomes]
rs1044575	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865029	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123761	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11123762	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11123763	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123764	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123765	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11123766	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11123770	0.89[EUR][1000 genomes]
rs1133977	0.91[EUR][1000 genomes]
rs1133978	0.91[EUR][1000 genomes]
rs11674894	0.86[EUR][1000 genomes]
rs11677247	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11677321	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11678456	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683107	0.92[EUR][1000 genomes]
rs11683188	0.90[EUR][1000 genomes]
rs11684507	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11684610	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11685759	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11688004	0.90[EUR][1000 genomes]
rs11689265	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11692336	0.91[EUR][1000 genomes]
rs11692669	0.85[EUR][1000 genomes]
rs11692699	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11693427	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11695379	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11695751	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11883676	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11890338	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11895749	0.91[EUR][1000 genomes]
rs11900670	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12464710	0.82[ASN][1000 genomes]
rs12467679	0.85[ASN][1000 genomes]
rs12473029	0.87[ASN][1000 genomes]
rs12477754	0.85[ASN][1000 genomes]
rs12477978	0.84[ASN][1000 genomes]
rs12613624	0.90[EUR][1000 genomes]
rs12619780	0.89[EUR][1000 genomes]
rs12621007	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12987548	0.89[EUR][1000 genomes]
rs12991189	0.84[EUR][1000 genomes]
rs12992218	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12992930	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12995473	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12999417	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13000731	0.91[EUR][1000 genomes]
rs13004491	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13008171	0.91[EUR][1000 genomes]
rs13008496	0.82[ASN][1000 genomes]
rs13009147	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13012481	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13018891	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13020339	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13022329	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13023479	0.83[AMR][1000 genomes]
rs13023501	0.86[EUR][1000 genomes]
rs13023744	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13026928	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13030961	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13031919	0.83[EUR][1000 genomes]
rs13033012	0.91[EUR][1000 genomes]
rs13035311	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1349778	0.85[ASN][1000 genomes]
rs1349779	0.87[ASN][1000 genomes]
rs13798	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1453563	0.90[EUR][1000 genomes]
rs1580068	0.85[ASN][1000 genomes]
rs17708218	0.88[ASN][1000 genomes]
rs17759607	0.90[EUR][1000 genomes]
rs1993230	0.88[ASN][1000 genomes]
rs2045057	0.88[ASN][1000 genomes]
rs2171359	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2171362	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2309524	0.88[ASN][1000 genomes]
rs2309581	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2516827	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516828	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516829	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516830	0.92[EUR][1000 genomes]
rs2516832	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2516833	0.92[EUR][1000 genomes]
rs2516834	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2516835	0.93[EUR][1000 genomes]
rs2516836	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2632260	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632261	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2632277	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2632283	0.93[EUR][1000 genomes]
rs2632284	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2964969	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34252185	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34272114	0.90[EUR][1000 genomes]
rs34766932	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35461437	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36071868	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4340581	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4347885	0.90[EUR][1000 genomes]
rs4402818	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4588238	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4622780	0.85[ASN][1000 genomes]
rs4850897	0.92[EUR][1000 genomes]
rs4851187	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4851188	0.90[EUR][1000 genomes]
rs6542852	0.82[ASN][1000 genomes]
rs6542858	0.85[ASN][1000 genomes]
rs6542863	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542864	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6542865	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6542866	0.93[EUR][1000 genomes]
rs6542868	0.92[EUR][1000 genomes]
rs6542869	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6542870	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704766	0.85[ASN][1000 genomes]
rs6708576	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6708878	0.92[EUR][1000 genomes]
rs6712704	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717723	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717729	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6726618	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6727749	0.92[EUR][1000 genomes]
rs6736064	0.85[ASN][1000 genomes]
rs6739579	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6741773	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6743355	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6751927	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6753063	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753650	0.83[EUR][1000 genomes]
rs6756650	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6757661	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6759354	0.85[ASN][1000 genomes]
rs720228	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs720229	0.89[EUR][1000 genomes]
rs7349217	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558004	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558239	0.82[ASN][1000 genomes]
rs7572660	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7577477	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7584809	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7604557	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605843	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7608938	0.92[EUR][1000 genomes]
rs8179690	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs896886	0.85[ASN][1000 genomes]
rs9308816	0.85[ASN][1000 genomes]
rs972768	0.88[ASN][1000 genomes]
rs9808541	0.80[ASN][1000 genomes]
rs9941561	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][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	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2969379	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs2969379	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs2969379	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs2969379	TSGA10	cis	Esophagus Mucosa	GTEx
rs2969379	TSGA10	cis	multi-tissue	Pritchard
rs2969379	TSGA10	cis	Thyroid	GTEx
rs2969379	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs2969379	TSGA10	cis	lung	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99772200-99795600	Weak transcription	Gastric	stomach
2	chr2:99772400-99776800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:99772400-99777000	Weak transcription	Placenta	Placenta
4	chr2:99772400-99781600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:99772400-99782000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:99772400-99782800	Weak transcription	Aorta	Aorta
7	chr2:99772400-99784000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:99772400-99784000	Weak transcription	Lung	lung
9	chr2:99772400-99784000	Weak transcription	Spleen	Spleen
10	chr2:99772400-99784800	Weak transcription	Pancreas	Pancrea
11	chr2:99772400-99786200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:99772400-99786200	Weak transcription	Psoas Muscle	Psoas
13	chr2:99772400-99795600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:99772400-99795600	Weak transcription	Small Intestine	intestine
15	chr2:99772400-99796400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:99772400-99796600	Weak transcription	Right Ventricle	heart
17	chr2:99772400-99796800	Weak transcription	Colonic Mucosa	Colon
18	chr2:99772400-99797000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr2:99772600-99778400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr2:99772600-99778400	Weak transcription	NHDF-Ad	bronchial
21	chr2:99772600-99778800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:99772600-99778800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:99772600-99781800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:99772600-99782200	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr2:99772600-99782200	Weak transcription	HUVEC	blood vessel
26	chr2:99772600-99783600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:99772600-99783600	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr2:99772600-99784000	Weak transcription	Thymus	Thymus
29	chr2:99772600-99784200	Weak transcription	HSMMtube	muscle
30	chr2:99772600-99784400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr2:99772600-99784800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr2:99772600-99784800	Weak transcription	NH-A	brain
33	chr2:99772600-99786200	Weak transcription	NHLF	lung
34	chr2:99772600-99795800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr2:99772600-99796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr2:99772600-99796600	Weak transcription	Fetal Kidney	kidney
37	chr2:99772600-99797000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr2:99772800-99779200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:99772800-99781600	Weak transcription	Duodenum Mucosa	Duodenum
40	chr2:99772800-99781800	Weak transcription	Osteobl	bone
41	chr2:99772800-99782200	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:99772800-99782600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:99772800-99783800	Weak transcription	HMEC	breast
44	chr2:99772800-99784000	Weak transcription	A549	lung
45	chr2:99772800-99786000	Weak transcription	Hela-S3	cervix
46	chr2:99772800-99796400	Weak transcription	Fetal Heart	heart
47	chr2:99773000-99781200	Weak transcription	Fetal Thymus	thymus
48	chr2:99773000-99796400	Weak transcription	Fetal Brain Male	brain
49	chr2:99773200-99777400	Strong transcription	Skeletal Muscle Female	skeletal muscle
50	chr2:99773200-99777600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links