Variant report

Variant	rs12190021
Chromosome Location	chr6:88427097-88427098
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:88410071..88413824-chr6:88426436..88430582,3	MCF-7	breast:
2	chr6:88409659..88413027-chr6:88424595..88428330,4	K562	blood:
3	chr6:88424923..88427514-chr6:88446888..88448552,2	K562	blood:

Variant related genes	Relation type
ENSG00000135334	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12203759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193470	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13200106	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13202825	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13203056	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs13203790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13206536	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13206957	1.00[JPT][hapmap]
rs13211833	1.00[ASN][1000 genomes]
rs13212076	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13219631	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs16879490	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16879507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16879510	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16879528	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs16879532	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs17504475	1.00[JPT][hapmap]
rs2307393	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs28381552	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs28752032	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34080809	1.00[ASN][1000 genomes]
rs35326820	1.00[ASN][1000 genomes]
rs35440627	1.00[ASN][1000 genomes]
rs35607770	1.00[ASN][1000 genomes]
rs35965137	1.00[ASN][1000 genomes]
rs3734908	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs3763176	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs55686846	0.94[AMR][1000 genomes]
rs61432898	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62417757	1.00[ASN][1000 genomes]
rs62419465	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62419466	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6900057	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs6902069	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6917424	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6927654	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6927826	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6929542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7738268	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7744213	0.85[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap]
rs7749032	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7760919	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758068	chr6:88358988-88441473	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	esv2759454	chr6:88358988-88441473	Strong transcription Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12190021	GSTM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:88412800-88432600	Weak transcription	Brain Angular Gyrus	brain
2	chr6:88420200-88436800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr6:88420400-88428400	Weak transcription	K562	blood
4	chr6:88422200-88432400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr6:88424400-88428200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr6:88424400-88428400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr6:88424400-88428600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:88424400-88432400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr6:88424600-88428200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr6:88424600-88428800	Weak transcription	NHLF	lung
11	chr6:88424600-88432400	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr6:88424600-88432400	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr6:88424600-88432400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr6:88424600-88432400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr6:88424600-88432800	Weak transcription	Fetal Thymus	thymus
16	chr6:88424600-88439200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr6:88424800-88428000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
18	chr6:88424800-88428600	Weak transcription	GM12878-XiMat	blood
19	chr6:88424800-88430400	Weak transcription	NHDF-Ad	bronchial
20	chr6:88425000-88428400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr6:88425000-88428600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:88425200-88432200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:88425200-88432200	Weak transcription	HSMM	muscle
24	chr6:88425200-88432400	Weak transcription	Hela-S3	cervix
25	chr6:88425600-88428400	Weak transcription	NHEK	skin
26	chr6:88425800-88428200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr6:88425800-88428200	Weak transcription	HMEC	breast
28	chr6:88425800-88428400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr6:88426200-88430200	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr6:88426800-88427200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr6:88426800-88427200	Enhancers	Brain Anterior Caudate	brain
32	chr6:88426800-88427200	Enhancers	NH-A	brain
33	chr6:88426800-88427400	Enhancers	Adipose Nuclei	Adipose
34	chr6:88426800-88427400	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr6:88426800-88427400	Enhancers	Osteobl	bone
36	chr6:88426800-88427600	Enhancers	Cortex derived primary cultured neurospheres	brain
37	chr6:88426800-88429000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
38	chr6:88426800-88432000	Enhancers	A549	lung
39	chr6:88427000-88427200	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr6:88427000-88427200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
41	chr6:88427000-88427400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:88427000-88427400	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr6:88427000-88427400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
44	chr6:88427000-88427400	Enhancers	Colonic Mucosa	Colon
45	chr6:88427000-88427400	Enhancers	Fetal Muscle Leg	muscle
46	chr6:88427000-88427400	Enhancers	Left Ventricle	heart
47	chr6:88427000-88427400	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:88427000-88427600	Enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr6:88427000-88427600	Enhancers	Brain Hippocampus Middle	brain
50	chr6:88427000-88427600	Enhancers	Right Atrium	heart

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