Variant report

Variant	rs32425
Chromosome Location	chr5:50099814-50099815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr16:1155873..1156568-chr5:50099716..50100332,2	MCF-7	breast:

Extended variants
information (count: 135 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:125)

rs_ID	r²[population]
rs10035164	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10036060	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10038842	0.84[EUR][1000 genomes]
rs10039272	0.80[ASN][1000 genomes]
rs10039639	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10043477	0.89[EUR][1000 genomes]
rs10044566	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10051561	0.80[ASN][1000 genomes]
rs10053011	1.00[CHB][hapmap]
rs10054381	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10056836	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10059085	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs10060850	0.88[ASN][1000 genomes]
rs10065432	0.80[ASN][1000 genomes]
rs10070517	0.86[EUR][1000 genomes]
rs10072398	0.80[ASN][1000 genomes]
rs10075034	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10085036	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs10471940	0.84[EUR][1000 genomes]
rs10471956	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10755235	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10940472	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10940497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11739828	0.92[EUR][1000 genomes]
rs11750241	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11750771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12188654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12519006	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521579	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12654776	0.81[ASN][1000 genomes]
rs13153982	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13164951	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs13173734	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13359044	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361410	0.88[ASN][1000 genomes]
rs1375127	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs152102	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154133	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs154134	1.00[ASN][1000 genomes]
rs154135	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154137	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs154140	1.00[ASN][1000 genomes]
rs154141	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs157970	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs16884018	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169497	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs171555	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17195388	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs182230	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1839128	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1988613	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs2354526	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2548581	1.00[CEU][hapmap];0.85[CHB][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548582	0.90[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2548583	0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs256341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2594706	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs26062	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs26065	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26066	1.00[EUR][1000 genomes]
rs26068	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs26069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs26071	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2697662	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs27156	0.95[EUR][1000 genomes]
rs27244	0.95[EUR][1000 genomes]
rs27245	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs27251	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs27254	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27264	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs27357	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs27389	1.00[CHB][hapmap]
rs27465	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27466	0.82[CHB][hapmap]
rs27467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs27468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27469	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27574	0.95[EUR][1000 genomes]
rs27609	0.91[EUR][1000 genomes]
rs27627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27725	0.96[EUR][1000 genomes]
rs28085	0.96[EUR][1000 genomes]
rs282549	1.00[EUR][1000 genomes]
rs282550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282551	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282552	1.00[CEU][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs282553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282557	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs282559	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs282561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28505342	0.80[ASN][1000 genomes]
rs28711235	0.80[ASN][1000 genomes]
rs32376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs32377	1.00[EUR][1000 genomes]
rs32378	1.00[EUR][1000 genomes]
rs32404	0.86[CEU][hapmap];1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs3763367	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs39613	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs39949	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4029420	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs41502	0.91[EUR][1000 genomes]
rs42284	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4865628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57079776	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs578198	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs59900589	0.84[EUR][1000 genomes]
rs62366937	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6450301	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6450359	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6869356	0.90[EUR][1000 genomes]
rs6872496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6886872	1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs6890519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6890869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs73101075	0.88[ASN][1000 genomes]
rs7449019	0.86[EUR][1000 genomes]
rs7711839	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7723361	0.83[CEU][hapmap]
rs7728126	0.80[ASN][1000 genomes]
rs7734389	0.84[EUR][1000 genomes]
rs895801	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs921210	1.00[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv1016237	chr5:49986171-50118816	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv537761	chr5:49986171-50118816	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
10	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs32425	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs32425	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50056800-50126400	Weak transcription	Rectal Smooth Muscle	rectum
2	chr5:50064000-50126800	Weak transcription	Osteobl	bone
3	chr5:50069600-50100000	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:50071400-50108000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr5:50071600-50138200	Weak transcription	Placenta	Placenta
6	chr5:50078200-50140000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr5:50083200-50116800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr5:50085400-50123800	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr5:50085400-50136200	Weak transcription	Thymus	Thymus
10	chr5:50090600-50100600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr5:50091200-50103600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr5:50091200-50104000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:50091200-50113800	Weak transcription	Fetal Stomach	stomach
14	chr5:50091200-50116200	Weak transcription	Stomach Smooth Muscle	stomach
15	chr5:50091200-50118800	Weak transcription	Spleen	Spleen
16	chr5:50091200-50123800	Weak transcription	Fetal Thymus	thymus
17	chr5:50091200-50124800	Weak transcription	Esophagus	oesophagus
18	chr5:50091200-50130400	Weak transcription	Pancreas	Pancrea
19	chr5:50091200-50133600	Weak transcription	Lung	lung
20	chr5:50091200-50136000	Weak transcription	Gastric	stomach
21	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
22	chr5:50091400-50101600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:50091400-50124000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr5:50091800-50104000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:50091800-50123400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr5:50093200-50112200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:50094000-50111200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr5:50094000-50123800	Weak transcription	HMEC	breast
29	chr5:50094200-50111600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr5:50095200-50100200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr5:50095600-50103200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr5:50095800-50114800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:50095800-50123400	Weak transcription	Fetal Lung	lung
34	chr5:50096000-50132200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:50097400-50100400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr5:50098000-50100200	ZNF genes & repeats	GM12878-XiMat	blood
37	chr5:50098000-50100400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr5:50098200-50100000	ZNF genes & repeats	Liver	Liver
39	chr5:50098400-50108000	Strong transcription	Primary monocytes fromperipheralblood	blood
40	chr5:50098800-50100000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr5:50098800-50100200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
42	chr5:50099000-50100000	Weak transcription	Primary neutrophils fromperipheralblood	blood
43	chr5:50099000-50100800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr5:50099200-50100200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr5:50099200-50100200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
46	chr5:50099200-50100200	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
47	chr5:50099200-50100200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:50099200-50100400	Strong transcription	Adipose Nuclei	Adipose
49	chr5:50099200-50107000	Strong transcription	Primary B cells from cord blood	blood
50	chr5:50099200-50108200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links