Variant report

Variant	rs6717629
Chromosome Location	chr2:187410817-187410818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:187406067..187412442-chr2:187438004..187442761,8	MCF-7	breast:
2	chr2:187409753..187412549-chr2:187463065..187465596,2	MCF-7	breast:
3	chr2:187405383..187412410-chr2:187452886..187457882,13	MCF-7	breast:
4	chr2:187406917..187410917-chr2:187453199..187456715,8	MCF-7	breast:
5	chr2:187410468..187412799-chr2:187439579..187442121,2	MCF-7	breast:
6	chr2:187392275..187395253-chr2:187409654..187411697,2	MCF-7	breast:
7	chr2:187408692..187413087-chr2:187413826..187419706,7	MCF-7	breast:
8	chr2:187408487..187411855-chr2:187414594..187417273,4	K562	blood:
9	chr2:187390194..187392854-chr2:187410483..187412106,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10194631	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10209563	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10209572	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10804007	0.89[CHD][hapmap]
rs10931247	0.80[ASN][1000 genomes]
rs11690463	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11695304	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11891731	0.80[ASN][1000 genomes]
rs12693452	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12693453	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13006571	0.89[CHD][hapmap]
rs13407441	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13428705	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1372649	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1375124	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1376783	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1584695	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333648	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17333690	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17333717	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17405738	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1839120	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992898	0.89[CHD][hapmap]
rs2083678	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2119861	0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs2119863	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];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2197138	0.89[CHD][hapmap]
rs2197787	0.84[CHB][hapmap];0.89[CHD][hapmap]
rs2370693	0.89[CHD][hapmap]
rs2887827	0.89[CHD][hapmap]
rs34723308	0.92[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3768778	0.83[CHD][hapmap]
rs3911084	0.89[CHD][hapmap]
rs4144784	0.91[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap]
rs4233788	0.89[CHD][hapmap]
rs4666706	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4666709	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4667104	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4667106	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6434188	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap]
rs66694735	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6717871	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6741369	0.89[CHD][hapmap]
rs6753278	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6755033	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68022965	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs68161763	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs68164840	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs719071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs719072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72903105	0.96[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72903112	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7572236	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7588772	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7591411	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs766633	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9333288	0.89[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv459988	chr2:187364878-187440683	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
4	nsv584031	chr2:187364878-187440683	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
5	nsv1004309	chr2:187389880-187455946	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv536082	chr2:187389880-187455946	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	nsv962124	chr2:187409210-187423691	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6717629	ITGAV	cis	parietal	SCAN
rs6717629	CYHR1	trans	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187405200-187411800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:187406600-187412000	Enhancers	HMEC	breast
3	chr2:187407800-187411000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:187408200-187412000	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr2:187408200-187412200	Enhancers	Hela-S3	cervix
6	chr2:187408400-187411400	Enhancers	HUES48 Cell Line	embryonic stem cell
7	chr2:187408400-187411400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr2:187408400-187411600	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr2:187408400-187412000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:187408600-187411000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr2:187408600-187411400	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:187408800-187412200	Enhancers	HSMM	muscle
13	chr2:187409200-187411200	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:187409200-187411200	Enhancers	HSMMtube	muscle
15	chr2:187409200-187412000	Enhancers	NH-A	brain
16	chr2:187409400-187411000	Flanking Active TSS	A549	lung
17	chr2:187409400-187412200	Enhancers	NHDF-Ad	bronchial
18	chr2:187409600-187411000	Enhancers	NHEK	skin
19	chr2:187409600-187411200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:187409600-187411400	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:187409600-187412000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:187409600-187412200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:187409600-187412200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:187409600-187412200	Enhancers	Muscle Satellite Cultured Cells	--
25	chr2:187409600-187412200	Enhancers	Osteobl	bone
26	chr2:187409800-187411600	Enhancers	HUVEC	blood vessel
27	chr2:187410000-187411000	Enhancers	H9 Cell Line	embryonic stem cell
28	chr2:187410000-187412200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr2:187410400-187411400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:187410600-187411400	Weak transcription	Adipose Nuclei	Adipose
31	chr2:187410600-187411600	Enhancers	Placenta	Placenta
32	chr2:187410600-187412000	Enhancers	NHLF	lung
33	chr2:187410600-187412200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:187410600-187412200	Enhancers	Psoas Muscle	Psoas
35	chr2:187410800-187411000	Enhancers	Fetal Kidney	kidney
36	chr2:187410800-187412200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:187410800-187412200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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