Variant report

Variant	rs1530756
Chromosome Location	chr7:112553037-112553038
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	chr7:112549685..112551374-chr7:112552430..112555294,2	MCF-7	breast:
2	chr7:112551586..112554572-chr7:112556093..112557637,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10238492	0.84[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs10243834	0.83[ASN][1000 genomes]
rs10249952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10272143	0.83[ASN][1000 genomes]
rs10273589	0.92[CEU][hapmap];0.82[CHB][hapmap];0.89[TSI][hapmap]
rs10275208	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280618	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10280825	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1044262	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs10500014	0.80[ASN][1000 genomes]
rs11762737	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11768408	0.84[CEU][hapmap];0.94[CHD][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11768787	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11769037	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1227163	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs1227174	0.82[CHB][hapmap]
rs1227181	0.82[CHB][hapmap]
rs1227190	0.82[CHB][hapmap]
rs1238698	0.82[CHB][hapmap]
rs12535487	0.82[CHB][hapmap]
rs12539085	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs1547554	1.00[CHB][hapmap]
rs17160078	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718967	1.00[CHB][hapmap]
rs17405723	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796492	0.82[CHB][hapmap]
rs1796493	0.82[CHB][hapmap]
rs1796516	0.82[CHB][hapmap]
rs1976897	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992988	0.84[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.90[ASN][1000 genomes]
rs1996843	1.00[CHB][hapmap]
rs2396570	0.92[CEU][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap]
rs2396574	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs2396583	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2457	0.82[CHB][hapmap]
rs2687267	1.00[CHB][hapmap]
rs2708296	0.82[CHB][hapmap]
rs35983930	0.80[ASN][1000 genomes]
rs3957315	0.84[CEU][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap]
rs3997335	1.00[CHB][hapmap]
rs494324	1.00[CHB][hapmap]
rs549688	0.82[CHB][hapmap]
rs552304	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs56012709	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564494	1.00[CHB][hapmap]
rs62491096	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62491097	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62491099	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6466421	0.82[CHB][hapmap]
rs6466423	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs672911	1.00[CHB][hapmap]
rs685259	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs6944843	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6953522	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs73196926	0.80[ASN][1000 genomes]
rs7777973	0.82[CHB][hapmap]
rs7781871	0.81[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.89[TSI][hapmap];0.83[YRI][hapmap];0.82[EUR][1000 genomes]
rs7789589	0.90[ASN][1000 genomes]
rs7803405	0.82[CHB][hapmap]
rs7806781	0.82[CHB][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap]
rs7808616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs821783	1.00[CHB][hapmap]
rs821785	1.00[CHB][hapmap]
rs821787	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs9969347	1.00[CHB][hapmap];0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531436	chr7:111856171-112585407	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	105 gene(s)	inside rSNPs	diseases
2	esv1794529	chr7:112400060-112588376	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	esv2754368	chr7:112483049-112588049	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2758131	chr7:112492127-112768628	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	esv2759556	chr7:112492127-112768628	Active TSS Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1530756	C7orf53	cis	parietal	SCAN

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:112507400-112556800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr7:112519000-112557400	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr7:112522200-112571000	Weak transcription	Thymus	Thymus
4	chr7:112522400-112558400	Weak transcription	Gastric	stomach
5	chr7:112522400-112558800	Weak transcription	Lung	lung
6	chr7:112524200-112556800	Weak transcription	Colonic Mucosa	Colon
7	chr7:112530400-112576600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr7:112534800-112553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr7:112534800-112553600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr7:112535000-112555400	Weak transcription	Esophagus	oesophagus
11	chr7:112535600-112553800	Weak transcription	Placenta	Placenta
12	chr7:112538800-112565600	Weak transcription	Pancreas	Pancrea
13	chr7:112539000-112559400	Weak transcription	Fetal Stomach	stomach
14	chr7:112541400-112578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr7:112541600-112556200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr7:112543000-112557000	Weak transcription	HepG2	liver
17	chr7:112543400-112556000	Weak transcription	Fetal Thymus	thymus
18	chr7:112546400-112556200	Weak transcription	NHLF	lung
19	chr7:112546400-112566000	Weak transcription	Right Ventricle	heart
20	chr7:112546600-112553200	Weak transcription	Fetal Brain Male	brain
21	chr7:112546600-112555000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr7:112547000-112555600	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr7:112547400-112555400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr7:112548000-112554000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr7:112548600-112556800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr7:112548800-112556000	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr7:112548800-112556400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr7:112548800-112556400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr7:112549000-112555200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr7:112549000-112557400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr7:112549200-112569000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr7:112549200-112571000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr7:112549400-112574200	Weak transcription	Fetal Brain Female	brain
34	chr7:112549600-112556400	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr7:112549600-112565800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr7:112550200-112554000	Weak transcription	HSMMtube	muscle
37	chr7:112550400-112560200	Weak transcription	HUVEC	blood vessel
38	chr7:112550600-112555600	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr7:112550600-112555600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr7:112550800-112553600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
41	chr7:112550800-112553800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr7:112550800-112554200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr7:112551400-112553800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr7:112551400-112555000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr7:112551400-112555000	Weak transcription	Left Ventricle	heart
46	chr7:112551400-112556400	Weak transcription	Fetal Intestine Small	intestine
47	chr7:112551400-112566200	Weak transcription	Aorta	Aorta
48	chr7:112551600-112553200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr7:112551600-112553200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr7:112551600-112553200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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