Variant report

Variant	rs9310519
Chromosome Location	chr3:17576505-17576506
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	chr3:17574853..17577476-chr3:17578727..17581379,2	K562	blood:
2	chr3:17568665..17570764-chr3:17576211..17578088,2	K562	blood:

Extended variants
information (count: 176 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:163)

rs_ID	r²[population]
rs10510475	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs10510477	0.82[CEU][hapmap]
rs10510478	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs10865749	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11128829	0.85[CHB][hapmap]
rs11128830	0.85[CHB][hapmap]
rs11128833	0.85[CHB][hapmap]
rs11128836	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs11128837	0.82[CEU][hapmap]
rs11128838	0.87[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs11128839	0.85[CEU][hapmap]
rs11128841	0.88[CEU][hapmap]
rs11128848	0.82[CEU][hapmap]
rs11128849	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11128850	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11128852	0.85[CEU][hapmap]
rs1120412	1.00[ASN][1000 genomes]
rs11708391	1.00[ASN][1000 genomes]
rs11914537	0.85[CHB][hapmap]
rs11914797	0.82[CHB][hapmap]
rs11915560	0.85[CHB][hapmap]
rs11918295	0.85[CHB][hapmap]
rs11920557	0.82[CHB][hapmap]
rs11920751	0.85[CHB][hapmap]
rs11922534	0.85[CHB][hapmap]
rs11923589	0.85[CHB][hapmap]
rs11923635	0.85[CHB][hapmap]
rs11924970	0.85[CHB][hapmap]
rs11927654	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap]
rs11929394	0.85[CHB][hapmap]
rs12106762	0.85[CHB][hapmap]
rs12106770	0.85[CHB][hapmap]
rs12106899	0.85[CHB][hapmap]
rs12106900	0.85[CHB][hapmap]
rs12185952	0.85[CHB][hapmap]
rs12487248	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs12488687	1.00[ASN][1000 genomes]
rs12497320	0.82[CEU][hapmap]
rs12631291	0.82[CEU][hapmap];0.90[YRI][hapmap]
rs13061771	0.82[CEU][hapmap]
rs13065637	0.84[CEU][hapmap]
rs13076724	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs13083917	1.00[YRI][hapmap]
rs13085167	0.82[CEU][hapmap]
rs13096559	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs13097908	0.82[CEU][hapmap]
rs13318886	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.81[MKK][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs13320647	0.81[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.84[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13327810	0.81[TSI][hapmap]
rs1374197	0.86[CHB][hapmap];0.87[CHD][hapmap]
rs1446301	0.82[CHB][hapmap]
rs1446303	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1596863	0.85[CHB][hapmap]
rs17043556	0.85[CHB][hapmap]
rs17043558	0.85[CHB][hapmap]
rs17043565	0.85[CHB][hapmap]
rs17043568	0.85[CHB][hapmap]
rs17043571	0.85[CHB][hapmap]
rs17043574	0.85[CHB][hapmap]
rs17043578	0.85[CHB][hapmap]
rs17043579	0.85[CHB][hapmap]
rs17043623	0.85[CHB][hapmap]
rs17043631	0.85[CHB][hapmap]
rs17043638	0.85[YRI][hapmap]
rs17043643	0.85[CHB][hapmap]
rs17043652	0.85[CHB][hapmap]
rs17200818	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs17200839	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs1867772	0.84[CEU][hapmap];1.00[ASN][1000 genomes]
rs2028874	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];1.00[ASN][1000 genomes]
rs2121262	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs2348363	0.89[ASN][1000 genomes]
rs283936	0.90[ASN][1000 genomes]
rs35521582	0.85[ASN][1000 genomes]
rs4128509	0.82[CEU][hapmap]
rs4243835	0.82[CEU][hapmap]
rs4243836	0.82[CEU][hapmap]
rs4243838	0.82[CEU][hapmap]
rs4312642	1.00[ASN][1000 genomes]
rs4377510	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4484221	0.81[CEU][hapmap]
rs4513482	0.82[CEU][hapmap]
rs4566567	0.82[CEU][hapmap]
rs4602424	0.82[CEU][hapmap]
rs4627740	0.85[CHB][hapmap]
rs4637311	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4908958	0.81[CEU][hapmap]
rs4908963	0.85[YRI][hapmap]
rs4908965	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4908967	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs4908992	0.82[CEU][hapmap];0.85[YRI][hapmap]
rs4909012	0.81[CEU][hapmap]
rs62245947	0.90[ASN][1000 genomes]
rs6442682	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs6577616	0.82[CEU][hapmap]
rs6577619	0.81[CEU][hapmap]
rs6577622	0.82[CEU][hapmap]
rs6577643	0.82[CEU][hapmap]
rs6763593	0.94[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs6768637	0.82[CEU][hapmap]
rs6784025	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs6788763	0.81[TSI][hapmap]
rs6788957	0.85[CHB][hapmap]
rs6789697	1.00[ASW][hapmap];0.82[CEU][hapmap];0.83[LWK][hapmap];0.89[MKK][hapmap];0.85[YRI][hapmap]
rs6792443	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs6792589	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs6792747	0.85[CHB][hapmap]
rs6801690	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];1.00[ASN][1000 genomes]
rs6803999	0.85[CHB][hapmap]
rs6807020	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap];0.85[YRI][hapmap]
rs6809062	0.82[CEU][hapmap]
rs6810235	0.82[CEU][hapmap]
rs7427235	0.85[CHB][hapmap]
rs7432241	0.85[CHB][hapmap]
rs7614318	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7617683	0.82[CEU][hapmap];1.00[YRI][hapmap]
rs7618836	0.85[CHB][hapmap]
rs7619879	0.85[CHB][hapmap]
rs7623979	0.81[TSI][hapmap]
rs7625175	1.00[ASN][1000 genomes]
rs7625855	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7632240	0.81[CEU][hapmap]
rs7644020	0.81[TSI][hapmap]
rs7644389	0.81[TSI][hapmap]
rs7647905	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs7650295	0.85[CHB][hapmap]
rs7651998	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs7652792	1.00[ASN][1000 genomes]
rs8179891	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs8179983	0.82[CEU][hapmap]
rs9310516	1.00[ASN][1000 genomes]
rs9310520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9310524	1.00[ASN][1000 genomes]
rs9310526	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs9310528	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[MKK][hapmap];0.82[TSI][hapmap]
rs9681232	0.82[CEU][hapmap]
rs9756494	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9757339	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812199	0.81[TSI][hapmap]
rs9812906	0.81[TSI][hapmap]
rs9813532	1.00[ASN][1000 genomes]
rs9815204	0.85[CEU][hapmap];1.00[ASN][1000 genomes]
rs9817290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9820703	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9821318	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.92[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9823064	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9823767	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.84[TSI][hapmap];0.90[YRI][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9824952	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9835988	0.90[ASN][1000 genomes]
rs9839588	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9843640	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[ASN][1000 genomes]
rs9847477	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9848610	0.81[TSI][hapmap]
rs9848766	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs9850127	0.95[YRI][hapmap]
rs9851302	0.85[CHB][hapmap]
rs9851518	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9864494	0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.95[ASN][1000 genomes]
rs9874826	0.89[ASN][1000 genomes]
rs9875973	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876715	0.82[CHB][hapmap]
rs9878954	0.81[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs9882273	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876590	chr3:17230884-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2755406	chr3:17237396-17589896	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv876591	chr3:17246392-17671992	Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv869378	chr3:17338236-17576692	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv915606	chr3:17357042-17668263	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv999568	chr3:17360261-17594750	Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv999460	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv536510	chr3:17360261-17720103	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv876592	chr3:17369313-17604963	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	esv2755442	chr3:17372796-17589896	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv876593	chr3:17419843-17604963	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv3715	chr3:17514325-17578178	Enhancers ZNF genes & repeats Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv1013069	chr3:17560456-17783372	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9310519	LSM3	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:17530600-17587600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:17536600-17588000	Weak transcription	Left Ventricle	heart
3	chr3:17548600-17579200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr3:17550000-17583800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:17557600-17597200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr3:17560600-17579800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:17561000-17599000	Weak transcription	Pancreas	Pancrea
8	chr3:17562000-17586800	Weak transcription	A549	lung
9	chr3:17563200-17593400	Weak transcription	Aorta	Aorta
10	chr3:17571400-17578800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:17574800-17579400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:17575000-17581000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:17575000-17583200	Weak transcription	GM12878-XiMat	blood
14	chr3:17575000-17607600	Weak transcription	Dnd41	blood
15	chr3:17575000-17613400	Weak transcription	Primary B cells from peripheral blood	blood
16	chr3:17575600-17581000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:17575800-17576600	Weak transcription	Brain Angular Gyrus	brain
18	chr3:17576000-17576800	Enhancers	Brain Anterior Caudate	brain
19	chr3:17576000-17577200	Enhancers	Fetal Heart	heart
20	chr3:17576000-17577400	Enhancers	Ovary	ovary
21	chr3:17576200-17576600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:17576200-17576800	Enhancers	Rectal Smooth Muscle	rectum
23	chr3:17576200-17577000	Enhancers	Pancreatic Islets	Pancreatic Islet
24	chr3:17576200-17577200	Enhancers	Fetal Brain Male	brain
25	chr3:17576400-17577000	Enhancers	Brain Substantia Nigra	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links