Variant report

Variant	rs12537977
Chromosome Location	chr7:102539230-102539231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:102537736..102539276-chr7:102622119..102624837,2	MCF-7	breast:

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs10228495	0.86[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap]
rs10241865	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10242028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10250490	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10271157	0.96[ASN][1000 genomes]
rs10271184	1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs10273725	0.91[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs10279449	1.00[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10808120	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1100046	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11514917	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11972261	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap]
rs11976237	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap]
rs11978799	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11981980	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs12666317	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs12668434	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs13233521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13242493	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs1541519	0.95[CHB][hapmap];0.98[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs1608651	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs17136090	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs1829957	0.85[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2190673	0.96[ASN][1000 genomes]
rs2228686	0.81[ASN][1000 genomes]
rs2411056	0.85[ASN][1000 genomes]
rs2411059	0.89[ASN][1000 genomes]
rs28856331	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41501847	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs4296965	0.89[ASN][1000 genomes]
rs4620204	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4729860	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs4729873	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs56269620	0.89[ASN][1000 genomes]
rs59544295	0.86[ASN][1000 genomes]
rs59709436	0.86[ASN][1000 genomes]
rs6465876	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs6465878	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6465880	0.96[ASN][1000 genomes]
rs6945997	0.82[ASN][1000 genomes]
rs6946773	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs6947403	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6953980	0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs6960428	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6963104	0.89[ASW][hapmap];0.90[LWK][hapmap];0.88[MKK][hapmap]
rs6967790	0.81[LWK][hapmap];1.00[YRI][hapmap]
rs6969054	0.81[JPT][hapmap]
rs6978630	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs7778418	0.95[CHD][hapmap];0.81[JPT][hapmap]
rs7779145	0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs7780405	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs7780981	0.91[CHB][hapmap];0.98[CHD][hapmap];0.91[JPT][hapmap]
rs7782908	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7785272	0.86[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs7789252	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs7794668	1.00[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs7800548	1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs7804322	0.86[ASN][1000 genomes]
rs847646	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs847647	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs847648	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs847649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs847656	0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs847658	0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs865865	0.88[ASN][1000 genomes]
rs869332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs955992	0.82[ASN][1000 genomes]
rs9690473	1.00[YRI][hapmap]
rs9718453	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]

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	nsv1016563	chr7:101912320-102695860	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1028438	chr7:101912320-102704135	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv868996	chr7:102332827-102991361	ZNF genes & repeats Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
4	esv2752138	chr7:102358320-102787135	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv608058	chr7:102466741-102571713	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv464667	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
7	nsv608060	chr7:102486254-102624192	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
8	nsv5880	chr7:102505158-102550471	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12537977	DPY19L2P2	cis	parietal	SCAN
rs12537977	CUX1	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:102517000-102549600	Weak transcription	Gastric	stomach
2	chr7:102517200-102578200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:102522600-102549200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr7:102536800-102540000	Weak transcription	Ovary	ovary
5	chr7:102537400-102541000	Weak transcription	K562	blood
6	chr7:102537800-102540000	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr7:102537800-102540000	Enhancers	Primary hematopoietic stem cells	blood
8	chr7:102538000-102540400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr7:102538200-102539400	Weak transcription	Stomach Mucosa	stomach
10	chr7:102538400-102539600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr7:102538400-102539600	Enhancers	Fetal Muscle Leg	muscle
12	chr7:102538400-102542400	Weak transcription	Fetal Kidney	kidney
13	chr7:102538400-102553200	Weak transcription	Colon Smooth Muscle	Colon
14	chr7:102538800-102539600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:102539200-102540400	Enhancers	Monocytes-CD14+_RO01746	blood
16	chr7:102539200-102551800	Weak transcription	Fetal Lung	lung
17	chr7:102539200-102553000	Weak transcription	Right Atrium	heart

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