Variant report

Variant	rs7301515
Chromosome Location	chr12:122949673-122949674
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:122883342..122886247-chr12:122947542..122950684,3	MCF-7	breast:
2	chr12:122906584..122908969-chr12:122947316..122950216,3	MCF-7	breast:
3	chr12:122904060..122906537-chr12:122948950..122950891,2	MCF-7	breast:
4	chr12:122884680..122885194-chr12:122948931..122949700,2	Hela-S3	cervix:
5	chr12:122947417..122950530-chr12:122951037..122954189,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000130779	Chromatin interaction

Extended variants
information (count: 92 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10161534	0.83[EUR][1000 genomes]
rs10734915	0.83[EUR][1000 genomes]
rs10734918	0.92[EUR][1000 genomes]
rs10734924	0.89[TSI][hapmap]
rs10744192	0.88[EUR][1000 genomes]
rs10744208	0.90[EUR][1000 genomes]
rs10744209	0.91[EUR][1000 genomes]
rs10744210	0.92[EUR][1000 genomes]
rs10744211	0.84[CEU][hapmap];0.92[EUR][1000 genomes]
rs10744217	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10744220	0.86[EUR][1000 genomes]
rs10773075	0.88[TSI][hapmap]
rs10773088	0.83[CEU][hapmap]
rs10773103	0.84[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs10773104	0.86[EUR][1000 genomes]
rs10773152	0.84[CEU][hapmap];0.94[TSI][hapmap]
rs10773167	0.92[EUR][1000 genomes]
rs10773172	0.92[EUR][1000 genomes]
rs10773176	0.93[EUR][1000 genomes]
rs10773178	0.92[EUR][1000 genomes]
rs10773208	0.87[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10846664	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs10846699	0.84[CEU][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs10846746	0.87[EUR][1000 genomes]
rs10846764	0.88[EUR][1000 genomes]
rs10846792	0.91[EUR][1000 genomes]
rs10846830	0.92[EUR][1000 genomes]
rs10846920	0.86[EUR][1000 genomes]
rs10846921	0.89[CEU][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10846931	0.87[EUR][1000 genomes]
rs10846978	0.87[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10847179	0.82[TSI][hapmap]
rs10847415	0.84[ASW][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[LWK][hapmap];0.81[TSI][hapmap]
rs10998	0.82[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs11057421	0.82[ASW][hapmap]
rs11057786	0.87[EUR][1000 genomes]
rs11057797	0.87[EUR][1000 genomes]
rs11057882	0.90[EUR][1000 genomes]
rs11058034	0.93[EUR][1000 genomes]
rs11058209	0.81[EUR][1000 genomes]
rs11058226	0.89[CEU][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs11058233	0.85[EUR][1000 genomes]
rs11058251	0.90[EUR][1000 genomes]
rs11058282	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11058402	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11616082	0.89[EUR][1000 genomes]
rs11836188	0.86[EUR][1000 genomes]
rs12369858	0.82[CEU][hapmap];0.91[TSI][hapmap]
rs12372756	0.83[CEU][hapmap]
rs12423420	0.85[EUR][1000 genomes]
rs12425970	0.91[EUR][1000 genomes]
rs12581249	0.87[EUR][1000 genomes]
rs1473553	0.82[MEX][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1803290	0.86[EUR][1000 genomes]
rs1818050	0.87[EUR][1000 genomes]
rs1973463	0.94[EUR][1000 genomes]
rs2341439	0.84[CEU][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs28730465	0.85[EUR][1000 genomes]
rs34129612	0.90[EUR][1000 genomes]
rs3817011	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs4758643	0.92[EUR][1000 genomes]
rs4758644	0.93[EUR][1000 genomes]
rs4758645	0.92[EUR][1000 genomes]
rs4758646	0.89[EUR][1000 genomes]
rs4758648	0.84[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs4758662	0.92[EUR][1000 genomes]
rs4758666	0.84[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs4997380	0.84[CEU][hapmap];0.91[TSI][hapmap]
rs55834409	0.86[EUR][1000 genomes]
rs6416298	0.91[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6488933	0.81[EUR][1000 genomes]
rs6488939	0.85[EUR][1000 genomes]
rs6488951	0.88[EUR][1000 genomes]
rs6488958	0.84[CEU][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs6489002	0.92[EUR][1000 genomes]
rs6489156	0.84[TSI][hapmap]
rs6489157	0.84[TSI][hapmap]
rs7135419	0.92[EUR][1000 genomes]
rs7294559	0.84[CEU][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs7307735	0.84[TSI][hapmap]
rs7314638	0.87[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs7316114	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7398014	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7952868	0.86[EUR][1000 genomes]
rs7956480	0.85[TSI][hapmap]
rs7963773	0.82[EUR][1000 genomes]
rs7964138	0.95[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7969429	0.91[EUR][1000 genomes]
rs7974262	0.92[EUR][1000 genomes]
rs7975747	0.82[CEU][hapmap]
rs9788145	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv973945	chr12:122923254-122958354	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7301515	RNF34	cis	parietal	SCAN
rs7301515	GTF2H3	cis	cerebellum	SCAN
rs7301515	NME2P1	cis	cerebellum	SCAN
rs7301515	B3GNT4	cis	cerebellum	SCAN
rs7301515	UGT2B17	trans	lymphoblastoid	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122922800-122960400	Weak transcription	Right Atrium	heart
2	chr12:122938800-122957000	Weak transcription	Thymus	Thymus
3	chr12:122939600-122955200	Weak transcription	Fetal Thymus	thymus
4	chr12:122941200-122957200	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:122943600-122951400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr12:122944400-122957000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:122945800-122956000	Weak transcription	GM12878-XiMat	blood
8	chr12:122946800-122949800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr12:122947400-122951600	Enhancers	Placenta	Placenta
10	chr12:122948000-122949800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr12:122948200-122949800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:122948200-122949800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr12:122948200-122949800	Enhancers	A549	lung
14	chr12:122948200-122949800	Enhancers	NHEK	skin
15	chr12:122948200-122952000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr12:122948400-122949800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:122948400-122949800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr12:122948400-122949800	Enhancers	Muscle Satellite Cultured Cells	--
19	chr12:122948400-122949800	Enhancers	HMEC	breast
20	chr12:122948400-122949800	Enhancers	HUVEC	blood vessel
21	chr12:122948400-122949800	Enhancers	NHDF-Ad	bronchial
22	chr12:122948400-122949800	Enhancers	NHLF	lung
23	chr12:122948400-122950000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:122948600-122949800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:122948600-122949800	Enhancers	Stomach Mucosa	stomach
26	chr12:122948600-122950000	Enhancers	Primary monocytes fromperipheralblood	blood
27	chr12:122948600-122957000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr12:122948800-122951200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr12:122948800-122951400	Weak transcription	Esophagus	oesophagus
30	chr12:122948800-122955600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:122948800-122955800	Weak transcription	Fetal Intestine Small	intestine
32	chr12:122948800-122957000	Weak transcription	Fetal Intestine Large	intestine
33	chr12:122948800-122958000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr12:122948800-122958000	Weak transcription	Psoas Muscle	Psoas
35	chr12:122949000-122955800	Weak transcription	HSMM	muscle
36	chr12:122949200-122951200	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr12:122949200-122955600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:122949200-122955800	Weak transcription	HepG2	liver
39	chr12:122949400-122949800	Flanking Active TSS	Hela-S3	cervix
40	chr12:122949600-122949800	Enhancers	Primary neutrophils fromperipheralblood	blood
41	chr12:122949600-122949800	Enhancers	Pancreas	Pancrea
42	chr12:122949600-122949800	Enhancers	Small Intestine	intestine
43	chr12:122949600-122949800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
44	chr12:122949600-122949800	Enhancers	NH-A	brain
45	chr12:122949600-122949800	Enhancers	Osteobl	bone
46	chr12:122949600-122952600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:122949600-122955600	Weak transcription	Fetal Muscle Leg	muscle
48	chr12:122949600-122955800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr12:122949600-122957000	Weak transcription	Lung	lung

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