Variant report

Variant	rs7307961
Chromosome Location	chr12:83390921-83390922
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	chr12:83077655..83080172-chr12:83389847..83391869,2	MCF-7	breast:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10082865	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs10778925	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs10778926	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10778928	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs10778931	0.92[CEU][hapmap]
rs10862540	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs10862541	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs10862542	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs11115527	0.92[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap]
rs1369035	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1484992	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1617818	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1619500	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1623131	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1624819	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655593	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs1655597	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655598	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655599	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655601	1.00[CHB][hapmap]
rs1655602	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655603	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655604	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1655606	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1682577	0.88[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];0.92[JPT][hapmap];0.94[TSI][hapmap]
rs1682584	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1682585	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1682586	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs1682589	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1682600	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1682601	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1682602	1.00[CHB][hapmap];0.93[CHD][hapmap];0.92[JPT][hapmap]
rs1682604	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs1796145	1.00[CHB][hapmap];0.89[JPT][hapmap]
rs1796146	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1796175	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs1796176	0.82[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1796194	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs1796195	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1796196	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1796197	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1796199	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1796205	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs1796206	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs1821443	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs1836247	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap]
rs2019742	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]
rs2082648	1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2403054	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap]
rs2952614	0.91[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs3940515	1.00[CHB][hapmap]
rs7974003	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs963363	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs963364	1.00[CHB][hapmap];0.92[CHD][hapmap];0.92[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv521849	chr12:83013783-83991479	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv469490	chr12:83089431-83507269	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
3	nsv559542	chr12:83089431-83507269	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
4	nsv832472	chr12:83248283-83419753	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
5	nsv559557	chr12:83334204-83453620	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
6	nsv1047239	chr12:83362299-83444855	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	n/a
7	esv3428924	chr12:83390171-83392369	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7307961	ABP1	trans	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:83358400-83397600	Weak transcription	Brain Anterior Caudate	brain
2	chr12:83358400-83409200	Weak transcription	Brain Angular Gyrus	brain
3	chr12:83358600-83394200	Weak transcription	Fetal Muscle Leg	muscle
4	chr12:83358600-83399600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:83358600-83409400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr12:83367400-83391800	Weak transcription	Small Intestine	intestine
7	chr12:83368800-83393800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr12:83368800-83399200	Weak transcription	Esophagus	oesophagus
9	chr12:83375600-83405600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr12:83377600-83400000	Weak transcription	Stomach Smooth Muscle	stomach
11	chr12:83377600-83409400	Weak transcription	Brain Hippocampus Middle	brain
12	chr12:83377800-83410200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr12:83378200-83391800	Weak transcription	Fetal Heart	heart
14	chr12:83378400-83394200	Weak transcription	Lung	lung
15	chr12:83378400-83409600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:83378800-83409000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr12:83379200-83397000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr12:83379800-83393200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr12:83380000-83394200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr12:83380000-83403200	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr12:83380000-83409200	Weak transcription	Gastric	stomach
22	chr12:83380200-83397200	Weak transcription	Brain Substantia Nigra	brain
23	chr12:83381800-83399400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:83382000-83393000	Weak transcription	Fetal Lung	lung
25	chr12:83382400-83399000	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr12:83382600-83399200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr12:83384000-83397000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:83384800-83391000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:83386000-83404200	Weak transcription	Colon Smooth Muscle	Colon
30	chr12:83386200-83391400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr12:83386200-83403600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr12:83386600-83394200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr12:83388200-83394200	Weak transcription	Fetal Stomach	stomach
34	chr12:83388400-83400800	Weak transcription	Fetal Kidney	kidney
35	chr12:83389200-83392800	Weak transcription	Monocytes-CD14+_RO01746	blood
36	chr12:83389800-83394400	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr12:83390000-83392000	Enhancers	Placenta Amnion	Placenta Amnion
38	chr12:83390200-83391000	Enhancers	Fetal Intestine Small	intestine
39	chr12:83390200-83409200	Weak transcription	Pancreas	Pancrea
40	chr12:83390400-83399200	Weak transcription	Fetal Intestine Large	intestine
41	chr12:83390800-83391800	Weak transcription	Stomach Mucosa	stomach

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