Variant report

Variant	rs10876092
Chromosome Location	chr12:51183311-51183312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51182843..51185421-chr12:51191723..51194223,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10783386	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10783387	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876084	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876087	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10876098	0.85[EUR][1000 genomes]
rs11169562	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169563	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169567	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169570	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169571	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169572	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169578	0.84[EUR][1000 genomes]
rs1129406	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11503907	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12372718	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34645899	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34863430	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35353300	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4307773	0.83[EUR][1000 genomes]
rs4986838	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61926299	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61926301	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61926303	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7133974	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7297504	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7304335	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7306677	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974517	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9943712	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3497481	chr12:51150734-51185125	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
2	esv3497482	chr12:51151798-51185232	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
3	esv3386327	chr12:51154734-51184232	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases
4	nsv899077	chr12:51160612-51188397	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS	Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
5	esv3414501	chr12:51174503-51534707	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10876092	ATF1	cis	Esophagus Muscularis	GTEx
rs10876092	ATF1	cis	Adipose Subcutaneous	GTEx
rs10876092	ATF1	cis	Artery Tibial	GTEx
rs10876092	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
5	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
6	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
9	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
10	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain
12	chr12:51160800-51190600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr12:51161000-51189800	Weak transcription	Ovary	ovary
14	chr12:51164400-51189600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr12:51172600-51190600	Weak transcription	Fetal Brain Male	brain
16	chr12:51173000-51189600	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:51173200-51190000	Weak transcription	Brain Cingulate Gyrus	brain
18	chr12:51175400-51192200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr12:51176000-51184400	Weak transcription	K562	blood
20	chr12:51176000-51189000	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr12:51176000-51189400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:51176000-51189400	Weak transcription	Brain Hippocampus Middle	brain
23	chr12:51176200-51189600	Weak transcription	Duodenum Mucosa	Duodenum
24	chr12:51176800-51189000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr12:51177400-51189200	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:51178200-51184200	Enhancers	Placenta	Placenta
27	chr12:51178400-51192400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:51178600-51189000	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr12:51178600-51189800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr12:51178800-51184200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:51178800-51192600	Weak transcription	Fetal Heart	heart
32	chr12:51179600-51189400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:51179800-51189200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr12:51179800-51189600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
35	chr12:51180000-51189600	Weak transcription	Left Ventricle	heart
36	chr12:51180000-51189600	Weak transcription	Stomach Smooth Muscle	stomach
37	chr12:51180200-51189600	Weak transcription	Small Intestine	intestine
38	chr12:51180600-51188800	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:51180600-51192800	Weak transcription	Esophagus	oesophagus
40	chr12:51180800-51185200	Weak transcription	Stomach Mucosa	stomach
41	chr12:51180800-51189600	Weak transcription	Lung	lung
42	chr12:51180800-51189600	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr12:51180800-51189800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr12:51180800-51189800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:51180800-51189800	Weak transcription	Gastric	stomach
46	chr12:51180800-51189800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr12:51180800-51190400	Weak transcription	Psoas Muscle	Psoas
48	chr12:51180800-51190800	Weak transcription	Colonic Mucosa	Colon
49	chr12:51180800-51191800	Weak transcription	Aorta	Aorta
50	chr12:51180800-51204400	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links