Variant report

Variant	rs852933
Chromosome Location	chr6:72118362-72118363
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-B3GAT2-3	chr6:72117911-72119956	XLOC_005764

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs1192038	0.89[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.81[ASN][1000 genomes]
rs1527714	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4707914	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6921100	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6927433	0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs828638	0.88[ASN][1000 genomes]
rs852932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852959	0.83[EUR][1000 genomes]
rs852963	0.94[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs852966	1.00[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.88[JPT][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs852967	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs875842	0.83[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830684	chr6:72094842-72282684	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	488 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs852933	GSTM1	trans	lymphoblastoid	seeQTL

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:72104000-72122000	Weak transcription	Fetal Stomach	stomach
2	chr6:72106000-72119600	Weak transcription	Lung	lung
3	chr6:72106000-72124800	Weak transcription	Fetal Muscle Leg	muscle
4	chr6:72106400-72126800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr6:72106400-72128600	Weak transcription	Fetal Brain Male	brain
6	chr6:72106600-72122000	Weak transcription	Brain Substantia Nigra	brain
7	chr6:72106800-72119400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:72106800-72122000	Weak transcription	Brain Cingulate Gyrus	brain
9	chr6:72106800-72128600	Weak transcription	Fetal Brain Female	brain
10	chr6:72106800-72128800	Weak transcription	Brain Germinal Matrix	brain
11	chr6:72107800-72118400	Weak transcription	Brain Hippocampus Middle	brain
12	chr6:72107800-72125000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr6:72114000-72119400	Weak transcription	Right Ventricle	heart
14	chr6:72114000-72124800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:72114200-72120600	Weak transcription	Aorta	Aorta
16	chr6:72114200-72122200	Weak transcription	Right Atrium	heart
17	chr6:72114200-72125000	Weak transcription	Brain Angular Gyrus	brain
18	chr6:72114600-72118600	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr6:72114600-72121600	Weak transcription	Colon Smooth Muscle	Colon
20	chr6:72114600-72121800	Weak transcription	Rectal Smooth Muscle	rectum
21	chr6:72114800-72118600	Weak transcription	Brain Anterior Caudate	brain
22	chr6:72114800-72118600	Weak transcription	Small Intestine	intestine
23	chr6:72114800-72119400	Weak transcription	Fetal Intestine Small	intestine
24	chr6:72114800-72121800	Weak transcription	Ovary	ovary
25	chr6:72115000-72119600	Weak transcription	Adipose Nuclei	Adipose
26	chr6:72115200-72118600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:72115200-72119600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:72115200-72121800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr6:72115400-72118800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:72115400-72121800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:72115400-72121800	Weak transcription	Fetal Heart	heart
32	chr6:72115400-72125200	Weak transcription	Fetal Intestine Large	intestine
33	chr6:72115600-72121400	Weak transcription	Liver	Liver
34	chr6:72115600-72123000	Genic enhancers	Muscle Satellite Cultured Cells	--
35	chr6:72115800-72120400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr6:72116200-72118600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:72116200-72118600	Enhancers	Osteobl	bone
38	chr6:72116200-72128600	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr6:72116400-72118600	Weak transcription	HSMMtube	muscle
40	chr6:72116600-72118600	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr6:72116600-72118600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:72116600-72119200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr6:72117000-72119000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:72117200-72118400	Enhancers	HUVEC	blood vessel
45	chr6:72117200-72119200	Weak transcription	Placenta	Placenta
46	chr6:72117200-72119800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr6:72117200-72122400	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr6:72117400-72118600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr6:72117400-72118600	Weak transcription	Stomach Smooth Muscle	stomach
50	chr6:72117400-72119200	Weak transcription	Fetal Lung	lung

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