Variant report

Variant	rs2197787
Chromosome Location	chr2:187490371-187490372
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187489867..187492397-chr2:187494469..187496444,2	MCF-7	breast:
2	chr2:187487385..187490996-chr2:187491673..187498174,5	K562	blood:
3	chr2:187488598..187492559-chr2:187493903..187496422,4	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10171481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10172499	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10174098	0.86[CHB][hapmap]
rs10194631	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs10209563	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs10209572	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs10804007	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11678190	0.84[CHB][hapmap]
rs11685758	0.83[CHB][hapmap]
rs12151442	0.84[CHB][hapmap]
rs12615659	0.84[CHB][hapmap]
rs12693453	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs12693454	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13001028	0.84[CHB][hapmap]
rs13006483	0.84[CHB][hapmap]
rs13006571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13028817	0.84[CHB][hapmap]
rs13030356	0.83[CHB][hapmap]
rs1372649	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs1375124	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs1448424	0.84[CHB][hapmap]
rs17334422	0.84[CHB][hapmap]
rs17406339	0.84[CHB][hapmap]
rs1992898	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2083678	0.84[CHB][hapmap]
rs2119861	0.83[CHD][hapmap]
rs2119863	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs2165656	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2197138	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[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];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3768777	0.86[CHB][hapmap];0.86[YRI][hapmap]
rs3768778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3768780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816386	0.84[CHB][hapmap]
rs3845712	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3911084	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3911239	0.86[CHB][hapmap]
rs4144784	0.83[CHD][hapmap]
rs4233788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6434188	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs6434190	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66630114	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717512	0.82[CHB][hapmap]
rs6717629	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs6717871	0.84[CHB][hapmap]
rs6741369	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]
rs719071	0.84[CHB][hapmap]
rs719072	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs72903148	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7419327	0.84[CHB][hapmap]
rs7577962	0.84[CHB][hapmap]
rs7588772	0.84[CHB][hapmap]
rs7589470	0.84[CHB][hapmap]
rs7596996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[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];0.85[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9333288	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333289	0.84[CHB][hapmap]
rs998972	0.84[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
rs2197787	ITGAV	cis	parietal	SCAN
rs2197787	ITGAV	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
2	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:187456400-187504000	Weak transcription	Fetal Muscle Trunk	muscle
4	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
5	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr2:187456800-187493400	Weak transcription	Brain Germinal Matrix	brain
7	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr2:187457200-187506000	Weak transcription	Liver	Liver
9	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
10	chr2:187458000-187511400	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:187459400-187505600	Weak transcription	NHLF	lung
13	chr2:187460200-187506200	Weak transcription	Small Intestine	intestine
14	chr2:187462600-187500600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:187462800-187515400	Weak transcription	Gastric	stomach
16	chr2:187464800-187536200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr2:187465800-187529200	Weak transcription	Dnd41	blood
18	chr2:187466800-187533200	Weak transcription	Colonic Mucosa	Colon
19	chr2:187467200-187528600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:187467400-187515800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr2:187467600-187506000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:187468800-187504000	Weak transcription	NHDF-Ad	bronchial
23	chr2:187469000-187501800	Weak transcription	Fetal Intestine Small	intestine
24	chr2:187471400-187502200	Weak transcription	NHEK	skin
25	chr2:187471600-187521000	Weak transcription	Aorta	Aorta
26	chr2:187476000-187519800	Weak transcription	K562	blood
27	chr2:187476600-187508600	Weak transcription	Lung	lung
28	chr2:187476800-187536200	Weak transcription	Fetal Brain Male	brain
29	chr2:187477400-187502400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr2:187478600-187502600	Weak transcription	GM12878-XiMat	blood
31	chr2:187482200-187533800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr2:187482600-187491800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:187482800-187501200	Weak transcription	Ovary	ovary
34	chr2:187482800-187501200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr2:187482800-187506000	Weak transcription	Fetal Kidney	kidney
36	chr2:187482800-187519600	Weak transcription	Brain Anterior Caudate	brain
37	chr2:187482800-187527800	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr2:187482800-187533200	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr2:187482800-187533600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr2:187482800-187533800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr2:187482800-187533800	Weak transcription	Psoas Muscle	Psoas
42	chr2:187483000-187494000	Weak transcription	Brain Angular Gyrus	brain
43	chr2:187483200-187491200	Weak transcription	Fetal Heart	heart
44	chr2:187483200-187502400	Weak transcription	Colon Smooth Muscle	Colon
45	chr2:187483400-187491200	Weak transcription	A549	lung
46	chr2:187483400-187493000	Weak transcription	Brain Substantia Nigra	brain
47	chr2:187483400-187494000	Weak transcription	Brain Cingulate Gyrus	brain
48	chr2:187483400-187519800	Weak transcription	Brain Hippocampus Middle	brain
49	chr2:187485600-187493800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr2:187486000-187492600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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