Variant report

Variant	rs645198
Chromosome Location	chr6:11589550-11589551
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:11585369..11588205-chr6:11589273..11592735,3	MCF-7	breast:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11755780	0.83[CEU][hapmap]
rs11963496	0.81[YRI][hapmap]
rs11965815	0.81[YRI][hapmap]
rs12192094	0.83[CEU][hapmap]
rs12198765	0.86[CEU][hapmap]
rs12198774	0.83[CEU][hapmap]
rs12198950	0.83[CEU][hapmap]
rs12200454	0.83[CEU][hapmap]
rs17397532	0.81[YRI][hapmap]
rs17476088	0.91[YRI][hapmap]
rs2025184	0.83[CEU][hapmap]
rs2140110	0.82[EUR][1000 genomes]
rs2327440	0.87[CEU][hapmap]
rs4711306	0.83[CEU][hapmap]
rs4713579	0.88[CHB][hapmap]
rs4713594	0.83[CEU][hapmap]
rs478147	0.94[CHB][hapmap]
rs490466	0.94[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];0.81[ASN][1000 genomes]
rs513870	0.88[CHB][hapmap]
rs534042	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs538808	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs554671	0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap]
rs555034	0.93[CHB][hapmap]
rs555742	1.00[CHB][hapmap];0.82[ASN][1000 genomes]
rs56055084	0.92[EUR][1000 genomes]
rs595877	0.81[MEX][hapmap]
rs598907	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs606402	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs620729	0.88[CHB][hapmap]
rs628980	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs637564	0.93[ASN][1000 genomes]
rs662296	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs675565	0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap]
rs678862	0.88[CHB][hapmap]
rs685384	0.94[CHB][hapmap]
rs6901328	0.83[CEU][hapmap]
rs6936326	0.83[CEU][hapmap];0.88[CHB][hapmap]
rs6941011	0.83[CEU][hapmap]
rs9348895	0.83[CEU][hapmap]
rs9348896	0.83[CEU][hapmap]
rs9357154	0.83[CEU][hapmap]
rs9394109	0.88[CHB][hapmap]
rs9394115	0.94[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap]
rs9394117	0.83[CEU][hapmap]
rs9394119	0.83[CEU][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs645198	GCNT2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11586200-11591200	Enhancers	NHLF	lung
2	chr6:11587000-11589800	Weak transcription	Fetal Lung	lung
3	chr6:11587000-11592400	Weak transcription	Liver	Liver
4	chr6:11587200-11589600	Weak transcription	A549	lung
5	chr6:11587200-11590400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:11587200-11590400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr6:11587200-11592600	Weak transcription	Ovary	ovary
8	chr6:11587200-11593000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:11587400-11589800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:11587400-11590000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:11587400-11591000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:11587400-11592200	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:11587400-11592400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr6:11587400-11592600	Weak transcription	Fetal Muscle Trunk	muscle
15	chr6:11587400-11592800	Weak transcription	Placenta	Placenta
16	chr6:11587400-11593600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:11587600-11589600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr6:11587600-11589800	Weak transcription	Fetal Stomach	stomach
19	chr6:11587600-11592800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr6:11588600-11590000	Genic enhancers	HSMM	muscle
21	chr6:11588600-11591000	Weak transcription	Aorta	Aorta
22	chr6:11589200-11589800	Transcr. at gene 5' and 3'	HSMMtube	muscle
23	chr6:11589400-11590000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr6:11589400-11590400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:11589400-11590600	Enhancers	Placenta Amnion	Placenta Amnion
26	chr6:11589400-11590800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr6:11589400-11591200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:11589400-11591200	Enhancers	HUVEC	blood vessel
29	chr6:11589400-11591200	Enhancers	NH-A	brain
30	chr6:11589400-11591200	Enhancers	NHDF-Ad	bronchial
31	chr6:11589400-11591200	Enhancers	Osteobl	bone
32	chr6:11589400-11591400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung

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