Variant report

Variant	rs10275208
Chromosome Location	chr7:112550025-112550026
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:112548050..112550695-chr7:112555857..112557634,3	MCF-7	breast:
2	chr7:112544603..112547960-chr7:112549294..112552785,5	K562	blood:
3	chr7:112428359..112430804-chr7:112549789..112551929,2	MCF-7	breast:
4	chr7:112549685..112551374-chr7:112552430..112555294,2	MCF-7	breast:
5	chr7:112544603..112547584-chr7:112548579..112552785,5	K562	blood:

Variant related genes	Relation type
ENSG00000146802	Chromatin interaction

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];0.81[TSI][hapmap]
rs10243834	0.83[ASN][1000 genomes]
rs10249952	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10272143	0.83[ASN][1000 genomes]
rs10273589	0.92[CEU][hapmap];0.82[CHB][hapmap];0.87[TSI][hapmap]
rs10280618	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10280825	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1044262	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs10500014	0.80[ASN][1000 genomes]
rs11762737	0.92[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11768408	0.84[CEU][hapmap];0.94[CHD][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11768787	0.83[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11769037	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[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]
rs1530756	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]
rs1547554	1.00[CHB][hapmap]
rs17160078	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][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];1.00[TSI][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1796492	0.82[CHB][hapmap]
rs1796493	0.82[CHB][hapmap]
rs1796516	0.82[CHB][hapmap]
rs1976897	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992988	0.84[CEU][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[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];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs2396574	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs2396583	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[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];0.81[TSI][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	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs564494	1.00[CHB][hapmap]
rs62491096	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62491097	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62491099	0.90[ASN][1000 genomes]
rs6466421	0.82[CHB][hapmap]
rs6466423	0.84[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];0.98[LWK][hapmap];0.87[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][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	0.88[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MKK][hapmap];0.92[TSI][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs7789589	0.90[ASN][1000 genomes]
rs7803405	0.82[CHB][hapmap]
rs7806781	0.82[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs7808616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[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
rs10275208	C7orf53	cis	parietal	SCAN

Chromatin state (count:107 , 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	chr7:112515400-112551000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr7:112516400-112551000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr7:112519000-112557400	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr7:112522200-112571000	Weak transcription	Thymus	Thymus
6	chr7:112522400-112551000	Weak transcription	Spleen	Spleen
7	chr7:112522400-112558400	Weak transcription	Gastric	stomach
8	chr7:112522400-112558800	Weak transcription	Lung	lung
9	chr7:112524200-112550800	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr7:112524200-112556800	Weak transcription	Colonic Mucosa	Colon
11	chr7:112529800-112550800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr7:112530200-112551000	Weak transcription	Brain Hippocampus Middle	brain
13	chr7:112530400-112576600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr7:112532400-112550800	Weak transcription	NHDF-Ad	bronchial
15	chr7:112534200-112551000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr7:112534400-112551000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr7:112534600-112551000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr7:112534800-112551000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr7:112534800-112551400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr7:112534800-112553200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr7:112534800-112553600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr7:112535000-112551000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr7:112535000-112551000	Weak transcription	Fetal Kidney	kidney
24	chr7:112535000-112555400	Weak transcription	Esophagus	oesophagus
25	chr7:112535600-112550800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr7:112535600-112553800	Weak transcription	Placenta	Placenta
27	chr7:112538400-112551000	Weak transcription	Colon Smooth Muscle	Colon
28	chr7:112538800-112565600	Weak transcription	Pancreas	Pancrea
29	chr7:112539000-112559400	Weak transcription	Fetal Stomach	stomach
30	chr7:112541400-112578800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr7:112541600-112551000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr7:112541600-112556200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr7:112543000-112557000	Weak transcription	HepG2	liver
34	chr7:112543400-112551000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr7:112543400-112556000	Weak transcription	Fetal Thymus	thymus
36	chr7:112545200-112550800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr7:112545400-112550400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr7:112545400-112550600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr7:112545400-112551000	Weak transcription	Left Ventricle	heart
40	chr7:112545400-112551000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr7:112545400-112551000	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr7:112545600-112551000	Weak transcription	Fetal Intestine Small	intestine
43	chr7:112545600-112551000	Weak transcription	Fetal Muscle Leg	muscle
44	chr7:112546200-112550800	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr7:112546400-112550600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr7:112546400-112550600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr7:112546400-112550800	Weak transcription	Primary B cells from peripheral blood	blood
48	chr7:112546400-112550800	Weak transcription	Fetal Muscle Trunk	muscle
49	chr7:112546400-112550800	Weak transcription	Osteobl	bone
50	chr7:112546400-112551000	Weak transcription	Primary B cells from cord blood	blood

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