Variant report

Variant	rs958340
Chromosome Location	chr12:9806654-9806655
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	POLR2A	chr12:9806630-9807205	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9798786..9803516-chr12:9803864..9807970,10	MCF-7	breast:
2	chr12:9799323..9802837-chr12:9803671..9808302,9	K562	blood:
3	chr12:9802928..9804462-chr12:9806298..9808980,2	K562	blood:

Variant related genes	Relation type
ENSG00000257027	TF binding region
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:78)

rs_ID	r²[population]
rs10466762	1.00[ASN][1000 genomes]
rs10772005	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772006	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844236	0.89[ASN][1000 genomes]
rs10844267	1.00[ASN][1000 genomes]
rs10844327	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844350	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844351	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844352	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844353	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844359	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844369	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11052207	1.00[ASN][1000 genomes]
rs11052209	1.00[ASN][1000 genomes]
rs11052234	1.00[ASN][1000 genomes]
rs11052235	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052245	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052254	1.00[ASN][1000 genomes]
rs11052282	0.89[ASN][1000 genomes]
rs11608817	0.89[ASN][1000 genomes]
rs11830731	0.84[AFR][1000 genomes]
rs12310789	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322854	0.83[AFR][1000 genomes]
rs12366653	1.00[ASN][1000 genomes]
rs12366792	1.00[ASN][1000 genomes]
rs12809846	1.00[ASN][1000 genomes]
rs12820641	0.89[ASN][1000 genomes]
rs12830419	0.89[ASN][1000 genomes]
rs12831287	1.00[ASN][1000 genomes]
rs1560008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1560010	0.86[AFR][1000 genomes]
rs16913477	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1863871	1.00[ASN][1000 genomes]
rs2114869	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2162657	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34323946	0.89[ASN][1000 genomes]
rs34333636	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34833649	1.00[ASN][1000 genomes]
rs34981673	1.00[ASN][1000 genomes]
rs35015427	1.00[ASN][1000 genomes]
rs35098654	1.00[ASN][1000 genomes]
rs35181877	0.89[ASN][1000 genomes]
rs35280686	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35561167	1.00[ASN][1000 genomes]
rs35642909	1.00[ASN][1000 genomes]
rs35671537	1.00[ASN][1000 genomes]
rs35884213	1.00[ASN][1000 genomes]
rs55873283	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61916061	0.89[ASN][1000 genomes]
rs6488065	0.89[ASN][1000 genomes]
rs7132037	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7136821	0.89[ASN][1000 genomes]
rs7299738	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7302110	1.00[ASN][1000 genomes]
rs7302746	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7303246	0.89[ASN][1000 genomes]
rs7304321	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7304464	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7305937	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7309800	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310405	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310516	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310568	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7310790	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311421	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311574	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311945	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959406	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959726	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961262	1.00[ASN][1000 genomes]
rs7961416	1.00[ASN][1000 genomes]
rs7962321	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7967102	0.89[ASN][1000 genomes]
rs7973603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974871	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7978187	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919786	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9919787	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	esv2757489	chr12:9583455-9810764	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv917178	chr12:9637315-9820153	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs958340	RP11-705C15.2	cis	Whole Blood	GTEx
rs958340	LOC374443	Cis_1M	lymphoblastoid	RTeQTL
rs958340	RP11-705C15.2	cis	Esophagus Mucosa	GTEx
rs958340	RP11-705C15.3	cis	Whole Blood	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9801600-9811200	Weak transcription	Gastric	stomach
2	chr12:9801600-9815600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:9802200-9815200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
5	chr12:9802600-9807200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr12:9802600-9812800	Weak transcription	Ovary	ovary
7	chr12:9802600-9814400	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:9803000-9811200	Weak transcription	Fetal Intestine Small	intestine
9	chr12:9803000-9812200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr12:9803000-9816400	Weak transcription	Brain Germinal Matrix	brain
11	chr12:9803000-9816800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr12:9803000-9819800	Weak transcription	Fetal Brain Female	brain
13	chr12:9803000-9820200	Weak transcription	Brain Substantia Nigra	brain
14	chr12:9803000-9822200	Weak transcription	Small Intestine	intestine
15	chr12:9803200-9812400	Weak transcription	Liver	Liver
16	chr12:9803200-9813400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr12:9803600-9806800	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr12:9803600-9812200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
20	chr12:9804000-9806800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr12:9804000-9806800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr12:9804000-9814200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr12:9804200-9807800	Weak transcription	Aorta	Aorta
24	chr12:9804200-9811200	Weak transcription	Right Ventricle	heart
25	chr12:9804200-9812400	Weak transcription	Brain Anterior Caudate	brain
26	chr12:9804200-9813200	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr12:9804200-9814200	Weak transcription	Colonic Mucosa	Colon
28	chr12:9804200-9814600	Weak transcription	Lung	lung
29	chr12:9804200-9815000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr12:9804400-9806800	Enhancers	Primary neutrophils fromperipheralblood	blood
31	chr12:9804400-9806800	Weak transcription	NHLF	lung
32	chr12:9804400-9807000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr12:9804400-9807000	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr12:9804400-9807000	Weak transcription	Hela-S3	cervix
35	chr12:9804400-9809400	Weak transcription	Brain Hippocampus Middle	brain
36	chr12:9804400-9810800	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr12:9804400-9811200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr12:9804400-9811200	Weak transcription	Fetal Stomach	stomach
39	chr12:9804400-9811200	Weak transcription	Spleen	Spleen
40	chr12:9804400-9812200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:9804400-9812200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:9804400-9812200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr12:9804400-9814600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr12:9804400-9820400	Weak transcription	HUVEC	blood vessel
45	chr12:9804600-9820000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr12:9804600-9820000	Weak transcription	HMEC	breast
47	chr12:9804600-9820200	Weak transcription	NHEK	skin
48	chr12:9804800-9811200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr12:9805000-9806800	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr12:9805000-9813800	Weak transcription	K562	blood

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