Variant report

Variant	rs6764672
Chromosome Location	chr3:150255152-150255153
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1133494	0.90[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs12695957	0.88[AFR][1000 genomes]
rs13071114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs14434	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs16862785	0.84[YRI][hapmap]
rs1915942	0.83[EUR][1000 genomes]
rs1915943	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2049229	1.00[CHB][hapmap];0.81[CHD][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2090916	1.00[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.88[MEX][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2204113	0.82[JPT][hapmap]
rs2868945	0.87[CEU][hapmap]
rs2868946	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2868947	0.87[ASN][1000 genomes]
rs4681631	0.91[EUR][1000 genomes]
rs6440683	0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6440685	0.93[ASW][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs6440688	0.81[LWK][hapmap];0.96[YRI][hapmap]
rs6787881	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6790726	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7374917	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7628889	0.93[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7631671	1.00[ASW][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs7638500	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs7642917	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs8052	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9289818	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9289821	0.83[EUR][1000 genomes]
rs954068	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9809820	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs9820529	0.90[AMR][1000 genomes]
rs9865177	0.83[EUR][1000 genomes]
rs9871517	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][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	nsv532662	chr3:150180747-150633414	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs6764672	TM4SF4	cis	parietal	SCAN
rs6764672	COMMD2	cis	cerebellum	SCAN
rs6764672	EIF2A	cis	Thyroid	GTEx
rs6764672	EIF2A	cis	Esophagus Muscularis	GTEx
rs6764672	EIF2A	cis	Artery Tibial	GTEx
rs6764672	EIF2A	cis	lung	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150235400-150256600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:150246200-150260600	Weak transcription	Muscle Satellite Cultured Cells	--
3	chr3:150246400-150259000	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:150246400-150259200	Weak transcription	Fetal Lung	lung
5	chr3:150246400-150261800	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:150246400-150262600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr3:150247000-150259400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr3:150248400-150263200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:150248800-150262000	Weak transcription	Thymus	Thymus
10	chr3:150249600-150260400	Weak transcription	GM12878-XiMat	blood
11	chr3:150251200-150259400	Weak transcription	Fetal Brain Female	brain
12	chr3:150252600-150259000	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr3:150252600-150259000	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:150253200-150259000	Weak transcription	HSMMtube	muscle
15	chr3:150253400-150258800	Weak transcription	A549	lung
16	chr3:150253400-150259200	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:150253400-150259600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr3:150253600-150255800	Weak transcription	Stomach Mucosa	stomach
19	chr3:150254000-150259200	Weak transcription	HSMM	muscle
20	chr3:150254400-150259200	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:150254400-150262000	Weak transcription	Fetal Intestine Small	intestine
22	chr3:150254400-150262600	Weak transcription	Fetal Stomach	stomach
23	chr3:150254800-150259200	Weak transcription	Stomach Smooth Muscle	stomach
24	chr3:150254800-150259400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr3:150254800-150259400	Weak transcription	Hela-S3	cervix
26	chr3:150254800-150261400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr3:150255000-150259200	Weak transcription	Primary B cells from cord blood	blood
28	chr3:150255000-150261000	Weak transcription	Fetal Brain Male	brain

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