Variant report

Variant	rs10804005
Chromosome Location	chr2:187297391-187297392
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10194631	0.94[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10200873	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10209563	0.94[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10209572	0.94[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs10497668	0.82[ASN][1000 genomes]
rs10804007	0.83[CHD][hapmap]
rs10931247	0.83[EUR][1000 genomes]
rs11891731	0.86[EUR][1000 genomes]
rs12693453	0.94[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap]
rs12997583	0.83[CEU][hapmap]
rs13006571	0.83[CHD][hapmap]
rs1372649	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap]
rs1375124	0.94[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap]
rs1375323	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs1448854	0.85[TSI][hapmap]
rs1562646	0.85[TSI][hapmap]
rs16827719	0.89[ASN][1000 genomes]
rs1868384	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1992898	0.83[CHD][hapmap]
rs2044919	0.85[TSI][hapmap]
rs2083678	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs2099849	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2119861	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2119863	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2197138	0.83[CHD][hapmap]
rs2197787	0.83[CHD][hapmap]
rs2370663	0.89[ASN][1000 genomes]
rs2370693	0.83[CHD][hapmap]
rs2887827	0.83[CHD][hapmap]
rs3768776	0.83[TSI][hapmap]
rs3911084	0.83[CHD][hapmap]
rs4144784	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4233788	0.83[CHD][hapmap]
rs4365424	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4544390	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4666705	0.81[LWK][hapmap];0.85[TSI][hapmap]
rs55770081	0.89[ASN][1000 genomes]
rs57092996	0.89[ASN][1000 genomes]
rs57995640	0.89[ASN][1000 genomes]
rs58300265	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59376280	0.89[ASN][1000 genomes]
rs60201574	0.87[ASN][1000 genomes]
rs6434188	0.82[CHB][hapmap];0.94[CHD][hapmap]
rs66647013	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6717629	0.81[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs6717871	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6730232	0.85[ASN][1000 genomes]
rs6740632	0.81[LWK][hapmap];0.80[MKK][hapmap];0.85[TSI][hapmap]
rs6741214	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6741369	0.83[CHD][hapmap]
rs719071	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs719072	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs72895450	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs72897347	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73033500	0.86[ASN][1000 genomes]
rs73035219	0.89[ASN][1000 genomes]
rs73035226	0.89[ASN][1000 genomes]
rs73035248	0.89[ASN][1000 genomes]
rs73035254	0.89[ASN][1000 genomes]
rs73035266	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs73035270	0.89[ASN][1000 genomes]
rs73035271	0.89[ASN][1000 genomes]
rs73037534	0.82[ASN][1000 genomes]
rs7562659	0.81[LWK][hapmap];0.85[TSI][hapmap]
rs7577962	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs7588772	0.94[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap]
rs9333288	0.83[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv428067	chr2:187171324-187334779	Enhancers Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1005680	chr2:187244500-187320653	Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv536080	chr2:187244500-187320653	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1001927	chr2:187264940-187325667	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv997835	chr2:187265730-187327561	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv536081	chr2:187265730-187327561	Enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10804005	ITGAV	cis	parietal	SCAN
rs10804005	ZSWIM2	cis	cerebellum	SCAN
rs10804005	ITGAV	cis	cerebellum	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187279800-187300600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr2:187282400-187299200	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:187287200-187300800	Weak transcription	Ovary	ovary
4	chr2:187287400-187298000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:187288600-187301200	Weak transcription	Gastric	stomach
6	chr2:187289200-187300800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:187290200-187298200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr2:187290600-187304200	Weak transcription	Stomach Mucosa	stomach
9	chr2:187291600-187298800	Weak transcription	Fetal Intestine Large	intestine
10	chr2:187291800-187299200	Weak transcription	Primary B cells from cord blood	blood
11	chr2:187291800-187300400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr2:187291800-187301800	Weak transcription	GM12878-XiMat	blood
13	chr2:187292000-187298400	Weak transcription	Primary B cells from peripheral blood	blood
14	chr2:187292000-187301200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:187292400-187299000	Weak transcription	Primary T cells from cord blood	blood
16	chr2:187292400-187299000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr2:187292600-187299200	Weak transcription	Dnd41	blood
18	chr2:187293000-187300400	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr2:187293000-187304400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr2:187293200-187299200	Weak transcription	HepG2	liver
21	chr2:187293200-187302600	Weak transcription	Rectal Smooth Muscle	rectum
22	chr2:187293400-187297800	Weak transcription	Liver	Liver
23	chr2:187293600-187298000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr2:187293800-187322000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr2:187294200-187301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr2:187294800-187299200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr2:187295400-187302600	Weak transcription	Brain Anterior Caudate	brain
28	chr2:187295600-187302400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:187296000-187299400	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr2:187296000-187300000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:187296000-187300600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr2:187296200-187302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr2:187296400-187300200	Strong transcription	Fetal Intestine Small	intestine
34	chr2:187296600-187299000	Weak transcription	Duodenum Mucosa	Duodenum
35	chr2:187296800-187299200	Weak transcription	Adipose Nuclei	Adipose
36	chr2:187296800-187299200	Weak transcription	Aorta	Aorta
37	chr2:187296800-187300400	Weak transcription	Brain Cingulate Gyrus	brain
38	chr2:187297000-187299200	Weak transcription	Fetal Stomach	stomach
39	chr2:187297000-187299400	Weak transcription	Spleen	Spleen
40	chr2:187297200-187303200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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