Variant report

Variant	rs741200
Chromosome Location	chr12:9870415-9870416
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 118 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1008610	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs1044771	1.00[ASW][hapmap];0.81[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.85[JPT][hapmap];0.83[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10466829	0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10492165	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10492166	0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1056151	0.88[ASN][1000 genomes]
rs10743819	0.87[ASN][1000 genomes]
rs10743823	0.85[JPT][hapmap]
rs10772070	0.84[ASN][1000 genomes]
rs10772071	0.84[ASN][1000 genomes]
rs10772072	0.84[ASN][1000 genomes]
rs10772073	0.84[ASN][1000 genomes]
rs10772074	0.85[ASN][1000 genomes]
rs10772079	0.85[ASN][1000 genomes]
rs10772085	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10772087	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10772090	0.80[ASN][1000 genomes]
rs10772091	0.82[ASN][1000 genomes]
rs10772092	0.82[ASN][1000 genomes]
rs10772094	0.82[ASN][1000 genomes]
rs10772102	0.90[JPT][hapmap]
rs10844456	0.90[JPT][hapmap]
rs10844472	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs10844503	0.90[JPT][hapmap]
rs10844537	0.90[JPT][hapmap]
rs10844562	0.81[ASN][1000 genomes]
rs10844569	0.85[ASN][1000 genomes]
rs10844597	0.84[ASN][1000 genomes]
rs10844609	0.85[ASN][1000 genomes]
rs10844610	0.83[ASN][1000 genomes]
rs10844615	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs10844617	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs10844620	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs10844622	0.86[ASN][1000 genomes]
rs10844626	0.82[ASN][1000 genomes]
rs10844627	0.82[ASN][1000 genomes]
rs10844630	0.82[ASN][1000 genomes]
rs10844632	0.82[ASN][1000 genomes]
rs10844633	0.82[ASN][1000 genomes]
rs10844635	0.82[ASN][1000 genomes]
rs10844636	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10844637	0.82[ASN][1000 genomes]
rs10844638	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs10844657	0.90[JPT][hapmap]
rs11052372	0.84[CHD][hapmap];0.85[JPT][hapmap]
rs11052423	0.85[JPT][hapmap]
rs11052426	0.90[JPT][hapmap]
rs11052497	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs11052552	0.86[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap]
rs11052582	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11052710	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11052713	0.83[ASN][1000 genomes]
rs11052717	0.85[ASN][1000 genomes]
rs11052750	0.82[ASN][1000 genomes]
rs11052751	0.82[ASN][1000 genomes]
rs11052752	0.82[ASN][1000 genomes]
rs11052877	0.90[JPT][hapmap]
rs12227655	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs12228641	0.81[ASN][1000 genomes]
rs12304510	0.86[ASN][1000 genomes]
rs12317499	0.83[ASN][1000 genomes]
rs12424826	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12427310	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12582584	0.86[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1560011	0.82[CHD][hapmap]
rs17806710	0.90[JPT][hapmap]
rs1985788	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2012643	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2058560	0.85[ASN][1000 genomes]
rs2080206	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2080211	0.84[JPT][hapmap];0.86[ASN][1000 genomes]
rs2098298	0.91[CEU][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2114870	0.80[JPT][hapmap]
rs2114871	0.88[ASN][1000 genomes]
rs2192437	0.88[ASN][1000 genomes]
rs2268146	0.88[CHD][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2401390	0.85[ASN][1000 genomes]
rs2401391	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2401393	0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2401394	0.88[ASN][1000 genomes]
rs2401395	0.88[ASN][1000 genomes]
rs2894	0.88[ASN][1000 genomes]
rs2895988	0.91[ASW][hapmap];0.81[CEU][hapmap];0.88[ASN][1000 genomes]
rs3764021	0.86[CHD][hapmap];0.85[JPT][hapmap]
rs3764022	0.85[JPT][hapmap]
rs4763283	0.87[ASN][1000 genomes]
rs4763839	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4763840	0.86[CHB][hapmap];0.85[JPT][hapmap];0.96[ASN][1000 genomes]
rs4763879	0.80[ASW][hapmap];0.82[MKK][hapmap];0.85[YRI][hapmap]
rs61915472	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61915473	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7296241	0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs7306304	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7306557	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7307111	0.87[ASN][1000 genomes]
rs7310460	1.00[ASW][hapmap];0.80[CEU][hapmap];0.80[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs741199	0.85[ASN][1000 genomes]
rs7956831	0.85[ASN][1000 genomes]
rs7960328	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7964018	0.93[ASN][1000 genomes]
rs7970116	0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7973535	0.88[ASN][1000 genomes]
rs7973638	0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs7974396	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7976584	0.88[ASN][1000 genomes]
rs7977720	0.82[ASN][1000 genomes]
rs7977940	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs917911	0.85[JPT][hapmap];1.00[YRI][hapmap]
rs917913	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9332411	1.00[ASW][hapmap];0.81[CEU][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap]

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	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
2	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	nsv983235	chr12:9852218-9893776	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2757490	chr12:9855958-9888553	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv442255	chr12:9862078-9874924	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3693109	chr12:9863968-9876091	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	nsv8910	chr12:9865993-9872509	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv976571	chr12:9868953-9873977	Enhancers Transcr. at gene 5' and 3' Genic enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs741200	CLEC2D	Cis_1M	lymphoblastoid	RTeQTL
rs741200	CLECL1	cis	brain	BrainEAC
rs741200	CLECL1	cis	Nerve Tibial	GTEx
rs741200	CLECL1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9858000-9872200	Enhancers	Primary B cells from peripheral blood	blood
2	chr12:9861000-9873200	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
4	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr12:9864000-9873600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr12:9868400-9872600	Weak transcription	HUVEC	blood vessel
9	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:9869200-9874200	Weak transcription	K562	blood
11	chr12:9870200-9870600	Active TSS	GM12878-XiMat	blood
12	chr12:9870200-9871000	Flanking Active TSS	Primary B cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links