Variant report

Variant	rs7977720
Chromosome Location	chr12:9866349-9866350
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 128 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:121)

rs_ID	r²[population]
rs1008610	0.89[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs1044771	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10466829	0.89[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10492165	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10492166	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056151	0.83[ASN][1000 genomes]
rs10743819	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10743823	0.89[CEU][hapmap];0.86[JPT][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10772046	0.95[ASN][1000 genomes]
rs10772062	0.97[ASN][1000 genomes]
rs10772070	0.95[ASN][1000 genomes]
rs10772071	0.95[ASN][1000 genomes]
rs10772072	0.95[ASN][1000 genomes]
rs10772073	0.95[ASN][1000 genomes]
rs10772074	0.95[ASN][1000 genomes]
rs10772079	0.95[ASN][1000 genomes]
rs10772085	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10772087	0.88[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10772090	0.90[ASN][1000 genomes]
rs10772091	0.92[ASN][1000 genomes]
rs10772092	0.92[ASN][1000 genomes]
rs10772094	0.92[ASN][1000 genomes]
rs10772102	0.89[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs10772108	0.82[ASN][1000 genomes]
rs10844380	0.85[ASN][1000 genomes]
rs10844427	0.80[ASN][1000 genomes]
rs10844456	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10844468	0.95[ASN][1000 genomes]
rs10844472	0.83[ASN][1000 genomes]
rs10844503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10844537	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10844562	0.98[ASN][1000 genomes]
rs10844569	0.95[ASN][1000 genomes]
rs10844597	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10844609	0.95[ASN][1000 genomes]
rs10844610	0.93[ASN][1000 genomes]
rs10844615	0.89[CHB][hapmap];0.85[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10844617	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10844620	0.86[CHB][hapmap];0.89[JPT][hapmap];0.93[ASN][1000 genomes]
rs10844622	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10844626	0.92[ASN][1000 genomes]
rs10844627	0.92[ASN][1000 genomes]
rs10844630	0.92[ASN][1000 genomes]
rs10844632	0.92[ASN][1000 genomes]
rs10844633	0.92[ASN][1000 genomes]
rs10844635	0.92[ASN][1000 genomes]
rs10844636	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10844637	0.92[ASN][1000 genomes]
rs10844638	0.89[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs10844639	0.87[ASN][1000 genomes]
rs10844640	0.85[ASN][1000 genomes]
rs10844657	0.89[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10844682	0.82[ASN][1000 genomes]
rs10844706	0.80[JPT][hapmap]
rs11052372	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs11052423	1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs11052426	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11052497	0.83[ASN][1000 genomes]
rs11052552	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11052582	0.86[ASN][1000 genomes]
rs11052604	0.96[ASN][1000 genomes]
rs11052710	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11052713	0.93[ASN][1000 genomes]
rs11052717	0.95[ASN][1000 genomes]
rs11052750	0.92[ASN][1000 genomes]
rs11052751	0.92[ASN][1000 genomes]
rs11052752	0.92[ASN][1000 genomes]
rs11052756	0.86[ASN][1000 genomes]
rs11052877	0.90[JPT][hapmap]
rs12227655	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs12228641	0.98[ASN][1000 genomes]
rs12304510	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12317499	0.93[ASN][1000 genomes]
rs12424826	0.84[ASN][1000 genomes]
rs12427310	0.86[ASN][1000 genomes]
rs12582584	0.83[ASN][1000 genomes]
rs17806710	1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1985788	0.81[ASN][1000 genomes]
rs2012643	0.85[ASN][1000 genomes]
rs2058560	0.95[ASN][1000 genomes]
rs2080206	0.88[ASN][1000 genomes]
rs2080211	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs2098298	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2114870	1.00[CHB][hapmap];0.85[CHD][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs2114871	0.83[ASN][1000 genomes]
rs2192437	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2268146	0.86[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2401390	0.95[ASN][1000 genomes]
rs2401391	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2401393	0.89[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2401394	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2401395	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2894	0.83[ASN][1000 genomes]
rs2895988	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs3764021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3764022	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs4763283	0.81[ASN][1000 genomes]
rs4763839	0.81[ASN][1000 genomes]
rs4763840	0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs61915472	0.84[ASN][1000 genomes]
rs61915473	0.86[ASN][1000 genomes]
rs7296241	0.84[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs7306304	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7306557	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7307111	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7310460	0.81[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs741199	0.95[ASN][1000 genomes]
rs741200	0.82[ASN][1000 genomes]
rs7956831	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7960328	0.84[ASN][1000 genomes]
rs7964018	0.86[ASN][1000 genomes]
rs7968401	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7970116	0.89[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973535	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7973638	0.88[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7974396	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7976584	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7977940	0.83[ASN][1000 genomes]
rs917911	0.85[JPT][hapmap]
rs917913	0.86[ASN][1000 genomes]
rs9332411	0.84[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs7977720	CLEC4C	cis	parietal	SCAN
rs7977720	CLECL1	cis	Nerve Tibial	GTEx
rs7977720	GABARAPL1	cis	parietal	SCAN
rs7977720	CLEC2A	cis	parietal	SCAN
rs7977720	CLECL1	cis	lung	GTEx
rs7977720	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs7977720	CLEC2D	cis	multi-tissue	Pritchard
rs7977720	KLRG1	cis	parietal	SCAN
rs7977720	DCAL1	cis	multi-tissue	Pritchard
rs7977720	TAS2R31	cis	parietal	SCAN

Chromatin state (count:9 , 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	chr12:9859000-9870200	Enhancers	Primary B cells from cord blood	blood
3	chr12:9861000-9873200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr12:9861000-9874200	Weak transcription	Fetal Thymus	thymus
5	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:9861800-9868200	Enhancers	GM12878-XiMat	blood
7	chr12:9861800-9874000	Weak transcription	Primary T helper cells fromperipheralblood	blood
8	chr12:9864000-9873600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--

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