Variant report

Variant	rs10878102
Chromosome Location	chr12:64434014-64434015
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	chr12:64432833..64435222-chr12:64436511..64438802,2	MCF-7	breast:
2	chr12:64432506..64434524-chr12:64443772..64446923,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10444577	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11175238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1162788	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12228437	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1344400	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1378778	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1456046	0.88[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1565942	0.80[CHB][hapmap]
rs2168411	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2647908	0.85[ASN][1000 genomes]
rs28366579	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4553444	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4763134	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60987129	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6581529	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581530	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.86[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963940	0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7980267	0.90[CHB][hapmap];0.90[CHD][hapmap];0.90[TSI][hapmap];0.80[EUR][1000 genomes]
rs990309	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3351487	chr12:64420364-64763950	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64418600-64456400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr12:64428800-64450800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:64430200-64439800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:64431200-64437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr12:64432000-64466400	Weak transcription	Pancreas	Pancrea
6	chr12:64432400-64434200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr12:64432400-64434200	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr12:64432400-64434200	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr12:64432400-64434400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr12:64432600-64434400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
11	chr12:64432800-64434200	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:64433000-64434400	Enhancers	H1 Cell Line	embryonic stem cell
13	chr12:64433400-64435200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr12:64433400-64436400	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:64433600-64434200	Enhancers	NHLF	lung
16	chr12:64433600-64434400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:64433600-64434400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:64433600-64434400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr12:64433600-64436400	Weak transcription	Fetal Muscle Leg	muscle
20	chr12:64433600-64436400	Weak transcription	HSMM	muscle
21	chr12:64433600-64436600	Weak transcription	Fetal Kidney	kidney
22	chr12:64433600-64437800	Weak transcription	Duodenum Mucosa	Duodenum
23	chr12:64433600-64439400	Weak transcription	NHEK	skin
24	chr12:64433600-64439600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:64433600-64439800	Weak transcription	Esophagus	oesophagus
26	chr12:64433600-64449600	Weak transcription	Psoas Muscle	Psoas
27	chr12:64433600-64452400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:64433600-64460800	Weak transcription	Aorta	Aorta
29	chr12:64433600-64474200	Weak transcription	Left Ventricle	heart
30	chr12:64433800-64434200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr12:64433800-64434200	Weak transcription	Brain Germinal Matrix	brain
32	chr12:64433800-64434200	Weak transcription	Fetal Brain Male	brain
33	chr12:64433800-64434200	Enhancers	NHDF-Ad	bronchial
34	chr12:64433800-64434400	Enhancers	Stomach Mucosa	stomach
35	chr12:64433800-64435400	Weak transcription	Adipose Nuclei	Adipose
36	chr12:64433800-64436200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:64433800-64436400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr12:64433800-64436400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:64433800-64436400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:64433800-64436400	Weak transcription	Fetal Stomach	stomach
41	chr12:64433800-64436400	Weak transcription	Ovary	ovary
42	chr12:64433800-64436400	Weak transcription	Small Intestine	intestine
43	chr12:64433800-64436600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr12:64433800-64437600	Weak transcription	Fetal Brain Female	brain
45	chr12:64433800-64437600	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr12:64433800-64438000	Weak transcription	Fetal Intestine Small	intestine
47	chr12:64433800-64439600	Weak transcription	Brain Hippocampus Middle	brain
48	chr12:64433800-64449400	Weak transcription	HSMMtube	muscle
49	chr12:64433800-64452000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:64433800-64458600	Weak transcription	Stomach Smooth Muscle	stomach

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