Variant report

Variant	rs7306557
Chromosome Location	chr12:9877356-9877357
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:9876569..9878295-chr12:9885822..9888452,2	K562	blood:
2	chr12:9876110..9878240-chr12:9880296..9883371,3	K562	blood:
3	chr12:9792708..9795930-chr12:9875976..9879286,3	K562	blood:
4	chr12:9801303..9803979-chr12:9875830..9877610,2	K562	blood:

Variant related genes	Relation type
ENSG00000272917	Chromatin interaction
ENSG00000233719	Chromatin interaction
ENSG00000184293	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:106)

rs_ID	r²[population]
rs1008610	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs1044771	0.91[JPT][hapmap]
rs10466829	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10492165	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10492166	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743819	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10743823	1.00[CEU][hapmap];0.91[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10772046	0.89[ASN][1000 genomes]
rs10772062	0.91[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	0.96[ASN][1000 genomes]
rs10772079	0.96[ASN][1000 genomes]
rs10772085	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10772087	1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs10772090	0.92[ASN][1000 genomes]
rs10772091	0.94[ASN][1000 genomes]
rs10772092	0.94[ASN][1000 genomes]
rs10772094	0.94[ASN][1000 genomes]
rs10772102	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs10772108	0.85[ASN][1000 genomes]
rs10844456	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844468	0.89[ASN][1000 genomes]
rs10844503	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844537	0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10844562	0.92[ASN][1000 genomes]
rs10844569	0.96[ASN][1000 genomes]
rs10844597	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10844609	0.96[ASN][1000 genomes]
rs10844610	0.95[ASN][1000 genomes]
rs10844615	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10844617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10844620	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10844622	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10844626	0.94[ASN][1000 genomes]
rs10844627	0.94[ASN][1000 genomes]
rs10844630	0.94[ASN][1000 genomes]
rs10844632	0.94[ASN][1000 genomes]
rs10844633	0.94[ASN][1000 genomes]
rs10844635	0.94[ASN][1000 genomes]
rs10844636	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10844637	0.93[ASN][1000 genomes]
rs10844638	1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10844639	0.89[ASN][1000 genomes]
rs10844640	0.85[ASN][1000 genomes]
rs10844657	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs10844682	0.85[ASN][1000 genomes]
rs10844706	0.86[JPT][hapmap]
rs11052372	0.89[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11052423	0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs11052426	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11052552	0.89[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs11052582	0.80[ASN][1000 genomes]
rs11052604	0.90[ASN][1000 genomes]
rs11052710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11052713	0.95[ASN][1000 genomes]
rs11052717	0.96[ASN][1000 genomes]
rs11052750	0.94[ASN][1000 genomes]
rs11052751	0.94[ASN][1000 genomes]
rs11052752	0.94[ASN][1000 genomes]
rs11052756	0.87[ASN][1000 genomes]
rs11052877	0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12227655	0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12228641	0.92[ASN][1000 genomes]
rs12304510	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12317499	0.95[ASN][1000 genomes]
rs12427310	0.80[ASN][1000 genomes]
rs17806710	0.89[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1985788	0.87[ASN][1000 genomes]
rs2058560	0.96[ASN][1000 genomes]
rs2080206	0.82[ASN][1000 genomes]
rs2080211	0.90[JPT][hapmap]
rs2098298	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2114870	0.89[CHB][hapmap];0.85[JPT][hapmap];0.81[ASN][1000 genomes]
rs2192437	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2268146	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2401390	0.96[ASN][1000 genomes]
rs2401391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401393	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401394	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2401395	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2895988	0.85[JPT][hapmap]
rs3764021	0.89[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3764022	0.89[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs4763839	0.86[ASN][1000 genomes]
rs4763840	0.85[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs61915473	0.80[ASN][1000 genomes]
rs7296241	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7306304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307111	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7310460	0.91[JPT][hapmap]
rs741199	0.96[ASN][1000 genomes]
rs741200	0.88[ASN][1000 genomes]
rs7956831	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7964018	0.81[ASN][1000 genomes]
rs7968401	0.88[ASN][1000 genomes]
rs7970116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973535	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7973638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7974396	0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs7976584	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7977720	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs917911	0.81[CHB][hapmap];0.91[JPT][hapmap]
rs917913	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7306557	CLECL1	Cis_1M	lymphoblastoid	RTeQTL
rs7306557	CLECL1	cis	Nerve Tibial	GTEx
rs7306557	CLECL1	cis	Adipose Subcutaneous	GTEx
rs7306557	CLECL1	cis	lung	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9861600-9882400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr12:9864600-9883800	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr12:9868600-9879200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr12:9873600-9877600	Flanking Active TSS	GM12878-XiMat	blood
5	chr12:9874400-9877800	Weak transcription	NHEK	skin
6	chr12:9874400-9878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr12:9874400-9881400	Enhancers	Primary B cells from cord blood	blood
8	chr12:9874600-9878000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:9875000-9881200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:9875400-9877400	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:9875600-9880000	Weak transcription	HUVEC	blood vessel
12	chr12:9876800-9878200	Weak transcription	Primary monocytes fromperipheralblood	blood
13	chr12:9876800-9878200	Weak transcription	Primary B cells from peripheral blood	blood

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