Variant report

Variant	rs1462943
Chromosome Location	chr4:103265343-103265344
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:103265183..103267325-chr4:103351533..103354144,2	MCF-7	breast:
2	chr4:103264616..103268649-chr4:103270354..103274790,5	K562	blood:
3	chr4:103264486..103268305-chr4:103421576..103425286,5	K562	blood:
4	chr4:103264289..103266526-chr4:103747342..103750313,2	K562	blood:
5	chr4:103265265..103268309-chr4:103269283..103272314,4	K562	blood:
6	chr4:103263099..103266958-chr4:103348980..103352984,5	K562	blood:

Variant related genes	Relation type
ENSG00000260651	Chromatin interaction
ENSG00000248161	Chromatin interaction
ENSG00000241144	Chromatin interaction
ENSG00000109332	Chromatin interaction
ENSG00000246560	Chromatin interaction
ENSG00000109320	Chromatin interaction
ENSG00000138821	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10019247	0.82[EUR][1000 genomes]
rs10461136	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11097776	0.91[EUR][1000 genomes]
rs11097780	0.82[EUR][1000 genomes]
rs1117520	0.95[CEU][hapmap]
rs1117522	0.93[EUR][1000 genomes]
rs1159788	0.93[EUR][1000 genomes]
rs11728286	0.93[EUR][1000 genomes]
rs11730379	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11730944	0.90[EUR][1000 genomes]
rs11730958	0.92[EUR][1000 genomes]
rs11931217	0.87[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11935847	0.92[EUR][1000 genomes]
rs12499248	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500141	0.82[EUR][1000 genomes]
rs12505568	0.82[EUR][1000 genomes]
rs12510124	0.95[CEU][hapmap];0.92[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs13104988	0.82[EUR][1000 genomes]
rs13107285	0.93[EUR][1000 genomes]
rs13112930	0.86[EUR][1000 genomes]
rs13114804	0.82[EUR][1000 genomes]
rs13125848	0.92[EUR][1000 genomes]
rs13147260	0.85[EUR][1000 genomes]
rs1381893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1381894	0.86[EUR][1000 genomes]
rs1381895	0.86[EUR][1000 genomes]
rs1381897	0.85[EUR][1000 genomes]
rs1381899	0.93[EUR][1000 genomes]
rs1462948	0.93[EUR][1000 genomes]
rs1462949	0.92[EUR][1000 genomes]
rs1462950	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1462951	0.93[EUR][1000 genomes]
rs1462952	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1599684	0.93[EUR][1000 genomes]
rs1599685	0.93[EUR][1000 genomes]
rs1599686	0.84[EUR][1000 genomes]
rs1870952	0.91[CEU][hapmap];0.93[EUR][1000 genomes]
rs2054393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086004	0.93[EUR][1000 genomes]
rs2126625	0.94[EUR][1000 genomes]
rs233820	0.81[JPT][hapmap]
rs34663993	0.84[ASN][1000 genomes]
rs34835832	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4557261	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4699012	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4699019	0.92[EUR][1000 genomes]
rs4699021	0.92[EUR][1000 genomes]
rs4699024	0.92[EUR][1000 genomes]
rs4699026	0.91[CEU][hapmap];0.90[GIH][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs56202729	0.86[ASN][1000 genomes]
rs62329487	0.86[ASN][1000 genomes]
rs6533014	0.83[GIH][hapmap]
rs6814302	0.91[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs6835467	0.92[EUR][1000 genomes]
rs6843751	0.92[EUR][1000 genomes]
rs6844796	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6848517	0.86[CEU][hapmap];0.87[CHB][hapmap];0.86[JPT][hapmap]
rs7436937	0.95[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.93[JPT][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7657947	0.92[EUR][1000 genomes]
rs7661593	0.93[EUR][1000 genomes]
rs7683109	0.92[EUR][1000 genomes]
rs962399	0.93[EUR][1000 genomes]
rs984055	0.92[EUR][1000 genomes]
rs985989	0.94[CHB][hapmap];0.86[JPT][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1462943	GSTCD	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:103263400-103266800	Active TSS	Lung	lung
2	chr4:103263400-103266800	Active TSS	GM12878-XiMat	blood
3	chr4:103263600-103265400	Flanking Active TSS	K562	blood
4	chr4:103263600-103267600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr4:103263800-103265400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr4:103263800-103265800	Flanking Active TSS	Primary hematopoietic stem cells	blood
7	chr4:103263800-103267000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr4:103264000-103266000	Active TSS	Placenta	Placenta
9	chr4:103264000-103266800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr4:103264000-103267000	Active TSS	Hela-S3	cervix
11	chr4:103264200-103265600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
12	chr4:103264200-103266800	Active TSS	H9 Cell Line	embryonic stem cell
13	chr4:103264200-103266800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:103264200-103267000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:103264400-103265400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
16	chr4:103264400-103266000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr4:103264400-103266800	Active TSS	Right Atrium	heart
18	chr4:103264400-103267400	Active TSS	A549	lung
19	chr4:103264600-103265400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
20	chr4:103264600-103265400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
21	chr4:103264600-103265400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
22	chr4:103264600-103265400	Flanking Active TSS	Liver	Liver
23	chr4:103264600-103265400	Flanking Active TSS	HMEC	breast
24	chr4:103264600-103265600	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr4:103264600-103266800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
26	chr4:103264600-103266800	Active TSS	Rectal Mucosa Donor 31	rectum
27	chr4:103264600-103267000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
28	chr4:103264800-103265400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr4:103264800-103265400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
30	chr4:103264800-103265400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr4:103264800-103265400	Flanking Active TSS	Duodenum Mucosa	Duodenum
32	chr4:103264800-103265400	Bivalent/Poised TSS	Fetal Heart	heart
33	chr4:103264800-103265400	Flanking Active TSS	Fetal Thymus	thymus
34	chr4:103264800-103265800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
35	chr4:103264800-103266200	Flanking Active TSS	Primary B cells from cord blood	blood
36	chr4:103264800-103266600	Active TSS	Thymus	Thymus
37	chr4:103264800-103266600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr4:103264800-103266800	Active TSS	Dnd41	blood
39	chr4:103264800-103267400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:103264800-103267600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr4:103265000-103265400	Flanking Bivalent TSS/Enh	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr4:103265000-103265400	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
43	chr4:103265000-103265400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:103265000-103265400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr4:103265000-103265400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr4:103265000-103265400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
47	chr4:103265000-103265400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
48	chr4:103265000-103265400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr4:103265000-103265400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:103265000-103265400	Flanking Active TSS	Brain Hippocampus Middle	brain

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