Variant report

Variant	rs10876084
Chromosome Location	chr12:51164810-51164811
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51156235..51160771-chr12:51163731..51171865,12	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123268	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10783386	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10783387	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876087	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876092	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10876098	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11169506	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs11169523	0.82[CHB][hapmap]
rs11169524	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs11169562	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169563	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169567	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169570	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169571	1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169572	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11169578	0.94[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1129406	0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11503907	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12372718	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12427378	0.81[CHB][hapmap]
rs12818741	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs1316607	0.82[CHB][hapmap]
rs13378012	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2090852	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2139930	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs2280503	0.94[CHB][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs34645899	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34863430	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35353300	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3742062	0.94[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4307773	0.86[EUR][1000 genomes]
rs4388959	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs4986838	0.94[CHB][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61926299	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61926301	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61926303	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7133974	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7137845	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7297504	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7304335	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306677	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974517	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs876080	0.89[CHB][hapmap];0.90[JPT][hapmap]
rs9943712	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10876084	ATF1	cis	Artery Tibial	GTEx
rs10876084	DIP2B	Cis_1M	lymphoblastoid	RTeQTL
rs10876084	DIP2B	cis	multi-tissue	Pritchard
rs10876084	ATF1	cis	Adipose Subcutaneous	GTEx
rs10876084	ATF1	cis	Esophagus Muscularis	GTEx
rs10876084	KIAA1463	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51159000-51175200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr12:51159000-51180200	Weak transcription	Esophagus	oesophagus
3	chr12:51159200-51166400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:51159200-51166600	Weak transcription	Fetal Muscle Trunk	muscle
5	chr12:51159200-51174600	Weak transcription	Lung	lung
6	chr12:51159200-51179400	Weak transcription	Aorta	Aorta
7	chr12:51159200-51192600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:51159400-51192600	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr12:51159600-51165000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:51159600-51166600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:51159600-51189200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:51159800-51165200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:51159800-51173800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr12:51159800-51176200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr12:51159800-51178200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr12:51159800-51178400	Weak transcription	NHDF-Ad	bronchial
17	chr12:51159800-51180600	Weak transcription	Fetal Lung	lung
18	chr12:51159800-51189600	Weak transcription	Spleen	Spleen
19	chr12:51159800-51190400	Weak transcription	Fetal Kidney	kidney
20	chr12:51159800-51191200	Weak transcription	Rectal Smooth Muscle	rectum
21	chr12:51160000-51165000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr12:51160000-51171200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr12:51160000-51174800	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr12:51160000-51174800	Weak transcription	Osteobl	bone
25	chr12:51160000-51175000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr12:51160000-51179200	Weak transcription	HSMMtube	muscle
27	chr12:51160000-51179800	Weak transcription	Small Intestine	intestine
28	chr12:51160000-51189800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr12:51160000-51190800	Weak transcription	Right Ventricle	heart
30	chr12:51160200-51165000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr12:51160200-51171000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:51160200-51171200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:51160200-51172600	Weak transcription	Brain Hippocampus Middle	brain
34	chr12:51160200-51172800	Weak transcription	HSMM	muscle
35	chr12:51160200-51174200	Weak transcription	Left Ventricle	heart
36	chr12:51160200-51175000	Weak transcription	Brain Anterior Caudate	brain
37	chr12:51160200-51178200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr12:51160200-51178400	Weak transcription	HMEC	breast
39	chr12:51160200-51179400	Weak transcription	Right Atrium	heart
40	chr12:51160200-51180200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
41	chr12:51160200-51189600	Weak transcription	Pancreas	Pancrea
42	chr12:51160200-51189800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr12:51160400-51165600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:51160400-51166600	Weak transcription	Fetal Brain Female	brain
45	chr12:51160600-51165000	Weak transcription	Adipose Nuclei	Adipose
46	chr12:51160600-51178200	Weak transcription	Psoas Muscle	Psoas
47	chr12:51160800-51165200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr12:51160800-51166000	Weak transcription	GM12878-XiMat	blood
49	chr12:51160800-51174800	Weak transcription	Liver	Liver
50	chr12:51160800-51189600	Weak transcription	Brain Angular Gyrus	brain

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