Variant report

Variant	rs4233788
Chromosome Location	chr2:187462581-187462582
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:187461746-187463096	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187352327..187355103-chr2:187460869..187462881,2	K562	blood:

Variant related genes	Relation type
ITGAV	TF binding region
ENSG00000224323	Chromatin interaction

Extended variants
information (count: 63 )
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];0.88[YRI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10172499	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10174098	0.86[CHB][hapmap]
rs10194631	0.89[CHD][hapmap]
rs10209563	0.89[CHD][hapmap]
rs10209572	0.89[CHD][hapmap]
rs10804007	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[JPT][hapmap];0.85[LWK][hapmap];0.86[MEX][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[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];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[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];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2197138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2197787	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]
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];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[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];0.85[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3768780	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3816386	0.85[CHB][hapmap]
rs3845712	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3911084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3911239	0.86[CHB][hapmap]
rs4144784	0.83[CHD][hapmap]
rs6434188	0.91[ASW][hapmap];0.89[CHD][hapmap]
rs6434190	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66630114	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6717512	0.83[CHB][hapmap]
rs6717629	0.89[CHD][hapmap]
rs6741369	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]
rs719072	0.83[CHD][hapmap]
rs72903148	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[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];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9333287	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9333288	1.00[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];0.98[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9333289	0.85[CHB][hapmap]
rs998972	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv1014203	chr2:187413781-187477586	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
5	nsv536083	chr2:187413781-187477586	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv2756507	chr2:187416494-187470494	Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	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
8	nsv818105	chr2:187423298-187481835	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	esv2753217	chr2:187424494-187470494	Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4233788	ITGAV	cis	cerebellum	SCAN
rs4233788	ITGAV	cis	parietal	SCAN

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187456000-187468400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:187456000-187470600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr2:187456000-187488200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr2:187456200-187468000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:187456200-187469600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr2:187456200-187508600	Weak transcription	Esophagus	oesophagus
7	chr2:187456200-187533000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr2:187456400-187466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr2:187456400-187466800	Weak transcription	Placenta	Placenta
10	chr2:187456400-187469600	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr2:187456400-187469800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr2:187456400-187488200	Weak transcription	Fetal Thymus	thymus
13	chr2:187456400-187504000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:187456600-187464200	Weak transcription	Fetal Stomach	stomach
15	chr2:187456600-187467600	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr2:187456600-187469400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:187456600-187469600	Weak transcription	Primary T cells from cord blood	blood
18	chr2:187456600-187514000	Weak transcription	Thymus	Thymus
19	chr2:187456600-187520000	Weak transcription	Primary T helper cells fromperipheralblood	blood
20	chr2:187456800-187468000	Weak transcription	Fetal Muscle Leg	muscle
21	chr2:187456800-187468000	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr2:187456800-187469200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:187456800-187493400	Weak transcription	Brain Germinal Matrix	brain
24	chr2:187456800-187534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr2:187457000-187464800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:187457000-187466600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr2:187457000-187466600	Weak transcription	Fetal Intestine Small	intestine
28	chr2:187457000-187467000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:187457200-187463600	Weak transcription	Adipose Nuclei	Adipose
30	chr2:187457200-187463800	Weak transcription	NHDF-Ad	bronchial
31	chr2:187457200-187464000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr2:187457200-187464200	Weak transcription	Pancreas	Pancrea
33	chr2:187457200-187466800	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr2:187457200-187468600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:187457200-187469400	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr2:187457200-187469600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:187457200-187506000	Weak transcription	Liver	Liver
38	chr2:187457200-187533800	Weak transcription	Spleen	Spleen
39	chr2:187457400-187463400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr2:187457400-187466800	Weak transcription	Fetal Intestine Large	intestine
41	chr2:187457400-187469600	Weak transcription	Right Atrium	heart
42	chr2:187457400-187472200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
43	chr2:187457600-187467000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:187458000-187464000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr2:187458000-187511400	Weak transcription	Primary T helper cells PMA-I stimulated	--
46	chr2:187458000-187529000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
47	chr2:187458400-187464400	Enhancers	Brain Substantia Nigra	brain
48	chr2:187458600-187463600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
49	chr2:187458600-187477000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:187458800-187464600	Enhancers	Fetal Heart	heart

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