Variant report

Variant	rs12501525
Chromosome Location	chr4:85786828-85786829
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	chr4:85782546..85784148-chr4:85786446..85788006,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11097028	0.92[AMR][1000 genomes]
rs12500519	0.94[ASN][1000 genomes]
rs12502559	0.92[AMR][1000 genomes]
rs12511112	0.87[CHD][hapmap];0.91[JPT][hapmap];0.91[TSI][hapmap]
rs13118671	1.00[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs13125323	0.90[AMR][1000 genomes]
rs1484661	0.95[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1508670	0.90[JPT][hapmap];0.92[AMR][1000 genomes]
rs17009317	0.93[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.81[YRI][hapmap];0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17009334	0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2046402	0.84[EUR][1000 genomes]
rs2218323	0.82[CHD][hapmap];0.91[JPT][hapmap]
rs2869216	0.83[CEU][hapmap];0.82[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs3098928	0.85[CHD][hapmap];0.91[JPT][hapmap];0.89[TSI][hapmap]
rs35190829	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3747680	0.90[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs4383611	0.93[ASW][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap]
rs4590017	0.93[ASW][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap]
rs55871210	0.92[AMR][1000 genomes]
rs58074983	0.92[AMR][1000 genomes]
rs6531783	0.87[ASW][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.90[LWK][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap]
rs67045782	0.84[EUR][1000 genomes]
rs67624868	0.87[AMR][1000 genomes]
rs6815917	0.90[AMR][1000 genomes]
rs6820517	0.80[AMR][1000 genomes]
rs6825852	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs6829807	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.88[ASN][1000 genomes]
rs6835046	0.82[EUR][1000 genomes]
rs6838727	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap]
rs6847067	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs6847564	0.95[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6858666	0.82[CHB][hapmap];0.85[CHD][hapmap];0.91[JPT][hapmap]
rs72664928	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs72664957	0.92[AMR][1000 genomes]
rs7685537	0.85[CHD][hapmap];0.91[JPT][hapmap]
rs7692223	0.82[JPT][hapmap]
rs7695054	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv427684	chr4:85668487-85863446	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12501525	HERC5	cis	cerebellum	SCAN
rs12501525	DMP1	cis	parietal	SCAN
rs12501525	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85722200-85787600	Weak transcription	Gastric	stomach
2	chr4:85723000-85821000	Weak transcription	Pancreas	Pancrea
3	chr4:85731400-85791600	Weak transcription	Lung	lung
4	chr4:85736400-85790600	Weak transcription	NHEK	skin
5	chr4:85770000-85792800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:85770200-85787000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr4:85770600-85787800	Weak transcription	Right Ventricle	heart
8	chr4:85771000-85791400	Weak transcription	HMEC	breast
9	chr4:85771000-85791600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:85771200-85791200	Weak transcription	A549	lung
11	chr4:85771200-85798200	Weak transcription	Left Ventricle	heart
12	chr4:85771200-85803200	Weak transcription	Brain Germinal Matrix	brain
13	chr4:85771600-85791600	Weak transcription	HepG2	liver
14	chr4:85773600-85791400	Weak transcription	NH-A	brain
15	chr4:85776000-85794200	Weak transcription	Fetal Lung	lung
16	chr4:85776200-85791400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr4:85776200-85791400	Weak transcription	Fetal Muscle Leg	muscle
18	chr4:85778000-85787000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr4:85778000-85787000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr4:85778000-85791200	Weak transcription	Osteobl	bone
21	chr4:85778000-85791400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr4:85778000-85791400	Weak transcription	Aorta	Aorta
23	chr4:85778000-85792200	Weak transcription	Colon Smooth Muscle	Colon
24	chr4:85778000-85800000	Weak transcription	Brain Cingulate Gyrus	brain
25	chr4:85778000-85813800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr4:85778000-85836600	Weak transcription	Rectal Smooth Muscle	rectum
27	chr4:85778200-85787000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr4:85778800-85832800	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr4:85779000-85787800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr4:85779200-85787400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr4:85779800-85828800	Weak transcription	Spleen	Spleen
32	chr4:85780200-85791400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr4:85781200-85795000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:85781400-85791200	Weak transcription	NHLF	lung
35	chr4:85781800-85787200	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr4:85781800-85787600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:85781800-85790200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr4:85781800-85790400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr4:85781800-85791200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr4:85781800-85791400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr4:85781800-85791400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr4:85781800-85791400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr4:85781800-85791400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr4:85781800-85791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr4:85781800-85791400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr4:85781800-85791400	Weak transcription	Placenta	Placenta
47	chr4:85781800-85791400	Weak transcription	HSMMtube	muscle
48	chr4:85781800-85791400	Weak transcription	NHDF-Ad	bronchial
49	chr4:85781800-85791600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr4:85781800-85794600	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links