Variant report

Variant	rs10879386
Chromosome Location	chr12:41336136-41336137
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41334681..41337499-chr12:41339129..41340865,2	MCF-7	breast:

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10219754	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10784948	0.97[AMR][1000 genomes]
rs10784951	0.97[ASN][1000 genomes]
rs10784952	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10784963	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784965	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10784981	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10879361	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10879368	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879384	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879388	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879390	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879400	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879415	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879418	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10879518	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10879519	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11178978	0.81[CEU][hapmap];0.85[CHB][hapmap];0.94[AMR][1000 genomes]
rs11179084	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179141	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179142	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11179157	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11179158	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11179184	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11179188	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11179205	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11179237	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11179277	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11179286	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11179300	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11179346	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11179364	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11179369	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11179419	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11179482	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12297682	1.00[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs12301044	0.94[AMR][1000 genomes]
rs12301270	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12315093	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12315256	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12367345	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12578703	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12579817	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12580874	0.94[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs17624585	0.82[CHB][hapmap]
rs2044090	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs28581358	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7137717	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7299744	0.97[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7305929	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7309797	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7954108	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7958047	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7958050	0.93[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7963005	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7968141	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7971217	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7974854	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs935105	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv826346	chr12:41313148-41374833	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41297200-41338600	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:41297400-41338600	Weak transcription	Brain Angular Gyrus	brain
3	chr12:41297400-41346400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr12:41305800-41336200	Weak transcription	NHEK	skin
5	chr12:41313400-41338400	Weak transcription	A549	lung
6	chr12:41317800-41356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr12:41318400-41341800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr12:41321800-41344600	Weak transcription	Ovary	ovary
9	chr12:41322600-41337800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:41328200-41338600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:41329200-41337600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr12:41332000-41339600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:41333400-41352800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:41336000-41336200	Enhancers	Duodenum Smooth Muscle	Duodenum

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