Variant report

Variant	rs1372649
Chromosome Location	chr2:187406760-187406761
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:187406067..187412442-chr2:187438004..187442761,8	MCF-7	breast:
2	chr2:187392659..187395517-chr2:187406680..187408986,2	MCF-7	breast:
3	chr2:187405383..187412410-chr2:187452886..187457882,13	MCF-7	breast:
4	chr2:187406154..187410015-chr2:187435632..187441776,6	MCF-7	breast:
5	chr2:187362564..187365025-chr2:187405176..187407721,2	K562	blood:
6	chr2:187406244..187408980-chr2:187422400..187424184,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138448	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10194631	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];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10209563	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10209572	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10804007	0.80[ASW][hapmap];0.83[CHD][hapmap]
rs10931247	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11685403	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11690463	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11695304	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11891731	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12693452	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12693453	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13006571	0.83[CHD][hapmap]
rs13407441	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13428705	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1375124	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1376783	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1584695	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17333648	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17333690	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17333717	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17405738	0.97[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1839120	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1992898	0.83[CHD][hapmap]
rs2083678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2099849	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2119861	0.93[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.80[EUR][1000 genomes]
rs2119863	0.88[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2197138	0.83[CHD][hapmap]
rs2197787	0.84[CHB][hapmap];0.83[CHD][hapmap]
rs2370693	0.83[CHD][hapmap]
rs2887827	0.83[CHD][hapmap]
rs34723308	0.90[AMR][1000 genomes]
rs3911084	0.83[CHD][hapmap]
rs4144784	0.88[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap]
rs4233788	0.83[CHD][hapmap]
rs4666706	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4666709	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4667104	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4667106	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6434188	1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[MEX][hapmap]
rs66694735	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6717629	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]
rs6717871	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][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]
rs6741214	0.87[ASN][1000 genomes]
rs6741369	0.83[CHD][hapmap]
rs6753278	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6755033	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs68022965	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68161763	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs68164840	0.99[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs719071	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs719072	0.82[ASW][hapmap];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];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72903105	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72903112	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7572236	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7577962	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7588772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7591411	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs766633	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
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	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1372649	ITGAV	cis	cerebellum	SCAN
rs1372649	ITGAV	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187363000-187408800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:187371000-187407800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:187386200-187408000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:187399400-187408200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr2:187405200-187406800	Enhancers	Muscle Satellite Cultured Cells	--
6	chr2:187405200-187407000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:187405200-187407200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:187405200-187407200	Enhancers	A549	lung
9	chr2:187405200-187407800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr2:187405200-187411800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr2:187405400-187406800	Enhancers	iPS-18 Cell Line	embryonic stem cell
12	chr2:187405400-187407000	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr2:187405400-187407000	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:187405600-187407000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:187405600-187407000	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr2:187405600-187407000	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:187405600-187407000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr2:187405600-187407000	Enhancers	Osteobl	bone
19	chr2:187405600-187408200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:187405800-187407000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr2:187406000-187407000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
22	chr2:187406000-187407000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr2:187406000-187407000	Enhancers	NH-A	brain
24	chr2:187406000-187407200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr2:187406000-187408200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr2:187406000-187410000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:187406200-187406800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:187406200-187407000	Enhancers	NHDF-Ad	bronchial
29	chr2:187406400-187406800	Weak transcription	HSMMtube	muscle
30	chr2:187406400-187408200	Weak transcription	HSMM	muscle
31	chr2:187406400-187408400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr2:187406400-187408600	Enhancers	HepG2	liver
33	chr2:187406400-187408600	Enhancers	HUVEC	blood vessel
34	chr2:187406600-187407400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr2:187406600-187408400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr2:187406600-187408600	Enhancers	NHEK	skin
37	chr2:187406600-187412000	Enhancers	HMEC	breast

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