Variant report

Variant	rs6741369
Chromosome Location	chr2:187487269-187487270
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187480029..187482174-chr2:187486614..187488319,2	MCF-7	breast:
2	chr2:187486374..187489207-chr2:187565002..187566617,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10171481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172499	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174098	0.86[CHB][hapmap]
rs10194631	0.89[CHD][hapmap]
rs10209563	0.89[CHD][hapmap]
rs10209572	0.89[CHD][hapmap]
rs10804007	0.80[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.95[MEX][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678190	0.85[CHB][hapmap]
rs11685758	0.84[CHB][hapmap]
rs12151442	0.85[CHB][hapmap]
rs12615659	0.85[CHB][hapmap]
rs12693453	0.89[CHD][hapmap]
rs12693454	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13001028	0.85[CHB][hapmap]
rs13006483	0.85[CHB][hapmap]
rs13006571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028817	0.85[CHB][hapmap]
rs13030356	0.84[CHB][hapmap]
rs1372649	0.83[CHD][hapmap]
rs1375124	0.89[CHD][hapmap]
rs1448424	0.85[CHB][hapmap]
rs17334422	0.85[CHB][hapmap]
rs17406339	0.85[CHB][hapmap]
rs1992898	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2119861	0.83[CHD][hapmap]
rs2119863	0.89[CHD][hapmap]
rs2165656	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197787	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887827	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768777	0.86[CHB][hapmap]
rs3768778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816386	0.85[CHB][hapmap]
rs3845712	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3911084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911239	0.86[CHB][hapmap]
rs4144784	0.83[CHD][hapmap]
rs4233788	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6434188	0.91[ASW][hapmap];0.89[CHD][hapmap]
rs6434190	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66630114	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717512	0.83[CHB][hapmap]
rs6717629	0.89[CHD][hapmap]
rs719072	0.83[CHD][hapmap]
rs72903148	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7419327	0.85[CHB][hapmap]
rs7589470	0.85[CHB][hapmap]
rs7596996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9333288	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333289	0.85[CHB][hapmap]
rs998972	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
3	nsv875552	chr2:187393729-187505486	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2756956	chr2:187416599-187492742	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6741369	ITGAV	cis	parietal	SCAN
rs6741369	ITGAV	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456000-187488200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
3	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr2:187456400-187488200	Weak transcription	Fetal Thymus	thymus
5	chr2:187456400-187504000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
7	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr2:187456800-187493400	Weak transcription	Brain Germinal Matrix	brain
9	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr2:187457200-187506000	Weak transcription	Liver	Liver
11	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
12	chr2:187458000-187511400	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr2:187459400-187505600	Weak transcription	NHLF	lung
15	chr2:187460200-187506200	Weak transcription	Small Intestine	intestine
16	chr2:187462600-187500600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr2:187462800-187515400	Weak transcription	Gastric	stomach
18	chr2:187464800-187536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:187465800-187529200	Weak transcription	Dnd41	blood
20	chr2:187466800-187533200	Weak transcription	Colonic Mucosa	Colon
21	chr2:187467200-187528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr2:187467400-187515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr2:187467600-187506000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:187468800-187504000	Weak transcription	NHDF-Ad	bronchial
25	chr2:187469000-187501800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:187469600-187488000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:187469600-187488200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr2:187470000-187488000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr2:187470000-187488600	Weak transcription	Fetal Stomach	stomach
30	chr2:187470200-187487600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr2:187470200-187488600	Weak transcription	Primary T cells from cord blood	blood
32	chr2:187470400-187487400	Weak transcription	HSMMtube	muscle
33	chr2:187471400-187487800	Weak transcription	Fetal Lung	lung
34	chr2:187471400-187488600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:187471400-187488600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr2:187471400-187502200	Weak transcription	NHEK	skin
37	chr2:187471600-187521000	Weak transcription	Aorta	Aorta
38	chr2:187472600-187488600	Weak transcription	HMEC	breast
39	chr2:187476000-187519800	Weak transcription	K562	blood
40	chr2:187476600-187487600	Weak transcription	HepG2	liver
41	chr2:187476600-187508600	Weak transcription	Lung	lung
42	chr2:187476800-187536200	Weak transcription	Fetal Brain Male	brain
43	chr2:187477400-187487800	Weak transcription	HSMM	muscle
44	chr2:187477400-187488600	Weak transcription	Primary hematopoietic stem cells	blood
45	chr2:187477400-187502400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr2:187478200-187488400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:187478600-187502600	Weak transcription	GM12878-XiMat	blood
48	chr2:187482200-187533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr2:187482600-187491800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr2:187482800-187490000	Weak transcription	Pancreas	Pancrea

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