Variant report

Variant	rs1500922
Chromosome Location	chr3:157052607-157052608
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156876376..156878675-chr3:157052120..157054386,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10513508	1.00[ASW][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10513509	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10513510	0.95[CEU][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs10513512	0.95[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs10804778	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10936078	0.82[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10936080	0.86[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10936081	1.00[ASW][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs10936083	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11918974	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12490192	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12494465	1.00[ASW][hapmap];0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12495519	0.84[ASN][1000 genomes]
rs12496269	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12632562	0.83[JPT][hapmap]
rs12634054	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12634689	0.90[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12635316	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs12637476	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1403106	0.83[JPT][hapmap]
rs1403108	0.94[JPT][hapmap]
rs1474281	0.95[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1500917	0.87[CEU][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1500918	0.86[CHB][hapmap];0.85[JPT][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1500924	0.82[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs1522392	1.00[ASW][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1568611	0.94[JPT][hapmap]
rs1587533	0.95[EUR][1000 genomes]
rs16827483	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs16827516	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16827530	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1875315	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2047648	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2047650	0.95[CEU][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2173824	0.95[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2874616	0.83[JPT][hapmap]
rs4680352	0.83[JPT][hapmap]
rs4680354	0.85[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs55865575	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56143236	0.85[ASN][1000 genomes]
rs56313302	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62278575	0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62278582	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278583	0.97[EUR][1000 genomes]
rs62278584	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278585	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278586	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278596	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62278597	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278598	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62278601	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs62278603	0.95[EUR][1000 genomes]
rs62281377	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62281379	0.89[ASN][1000 genomes]
rs62281383	0.89[ASN][1000 genomes]
rs6799567	0.82[CHB][hapmap];0.94[GIH][hapmap];0.89[JPT][hapmap];0.82[TSI][hapmap]
rs73156752	0.94[EUR][1000 genomes]
rs73156753	0.97[EUR][1000 genomes]
rs73156756	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73156757	0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73156759	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7631257	0.82[CHB][hapmap];0.94[JPT][hapmap];0.85[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs7649737	0.94[JPT][hapmap]
rs7652298	0.83[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1500922	C3orf55	cis	parietal	SCAN
rs1500922	PTX3	cis	parietal	SCAN
rs1500922	PTX3	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157036800-157053000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:157041000-157065600	Weak transcription	Pancreas	Pancrea
3	chr3:157048000-157054600	Enhancers	NHDF-Ad	bronchial
4	chr3:157048200-157057000	Weak transcription	Primary hematopoietic stem cells	blood
5	chr3:157050400-157054800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr3:157050600-157054600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:157051000-157053600	Enhancers	Osteobl	bone
8	chr3:157051000-157054000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:157051000-157054200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr3:157051000-157054800	Enhancers	Muscle Satellite Cultured Cells	--
11	chr3:157051000-157054800	Enhancers	NHLF	lung
12	chr3:157051000-157056200	Enhancers	HUVEC	blood vessel
13	chr3:157051200-157052800	Enhancers	H9 Cell Line	embryonic stem cell
14	chr3:157051400-157053400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr3:157051400-157054200	Enhancers	HSMM	muscle
16	chr3:157051400-157054400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr3:157051600-157053600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr3:157051600-157054800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:157051800-157053000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr3:157051800-157054200	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:157051800-157054600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr3:157052000-157054800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr3:157052200-157053000	Enhancers	iPS-18 Cell Line	embryonic stem cell
24	chr3:157052200-157053000	Weak transcription	NH-A	brain
25	chr3:157052400-157053200	Enhancers	iPS-20b Cell Line	embryonic stem cell
26	chr3:157052400-157053400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr3:157052400-157053400	Enhancers	Brain Hippocampus Middle	brain
28	chr3:157052400-157054400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:157052400-157054400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:157052600-157053800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:157052600-157054000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:157052600-157054200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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