Variant report

Variant	rs56181683
Chromosome Location	chr6:146286620-146286621
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:146284498-146286630	GM12891	blood:	n/a	n/a
2	STAT3	chr6:146286436-146286630	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:146054881..146058754-chr6:146284576..146286666,3	K562	blood:
2	chr6:146133534..146136752-chr6:146283932..146287911,4	K562	blood:
3	chr6:146051601..146058492-chr6:146282422..146286666,8	K562	blood:

Variant related genes	Relation type
SHPRH	TF binding region
ENSG00000118496	Chromatin interaction
ENSG00000235652	Chromatin interaction
ENSG00000270638	Chromatin interaction
ENSG00000112425	Chromatin interaction
ENSG00000270828	Chromatin interaction

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:157)

rs_ID	r²[population]
rs10223508	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10457792	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10457793	0.87[EUR][1000 genomes]
rs10457794	0.87[EUR][1000 genomes]
rs10457795	0.87[EUR][1000 genomes]
rs1062067	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1062068	0.85[EUR][1000 genomes]
rs10872582	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10872583	0.90[EUR][1000 genomes]
rs11155452	0.87[EUR][1000 genomes]
rs1133832	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11755334	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11760	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12194437	0.87[EUR][1000 genomes]
rs13198450	0.91[EUR][1000 genomes]
rs13204280	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1331636	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1331637	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1331639	0.87[EUR][1000 genomes]
rs1331643	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1331645	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1412081	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1474871	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1832362	0.81[ASN][1000 genomes]
rs2073287	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2144477	0.88[EUR][1000 genomes]
rs2144478	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2207785	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2224120	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2224121	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2243665	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2247206	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2247211	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2247317	0.85[ASN][1000 genomes]
rs2247429	0.85[EUR][1000 genomes]
rs2247666	0.86[EUR][1000 genomes]
rs2249147	0.81[ASN][1000 genomes]
rs2250387	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2253194	0.84[ASN][1000 genomes]
rs2253307	0.84[ASN][1000 genomes]
rs2253648	0.84[ASN][1000 genomes]
rs2253764	0.84[ASN][1000 genomes]
rs2253768	0.84[ASN][1000 genomes]
rs2253880	0.82[ASN][1000 genomes]
rs2253886	0.83[ASN][1000 genomes]
rs2253887	0.83[ASN][1000 genomes]
rs2254257	0.85[EUR][1000 genomes]
rs2254283	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2254288	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2256998	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265467	0.84[ASN][1000 genomes]
rs2265468	0.86[EUR][1000 genomes]
rs2265469	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2265471	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265472	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2265477	0.85[ASN][1000 genomes]
rs2265916	0.81[ASN][1000 genomes]
rs2265917	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265918	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2265919	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2328712	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2474356	0.98[EUR][1000 genomes]
rs2485632	0.83[ASN][1000 genomes]
rs2492855	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2748482	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2748483	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748484	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2748485	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2748486	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2748487	0.89[EUR][1000 genomes]
rs2748499	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2748500	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2748502	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777474	0.92[ASN][1000 genomes]
rs2777476	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2777477	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2777484	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814866	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2814867	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2814869	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2814874	0.98[EUR][1000 genomes]
rs2814875	0.98[EUR][1000 genomes]
rs2814876	0.98[EUR][1000 genomes]
rs2814877	0.98[EUR][1000 genomes]
rs2814879	0.84[ASN][1000 genomes]
rs2814880	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2892453	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3923579	0.88[EUR][1000 genomes]
rs3924498	0.89[EUR][1000 genomes]
rs3924499	0.89[EUR][1000 genomes]
rs3924502	0.88[EUR][1000 genomes]
rs4075694	0.91[EUR][1000 genomes]
rs4075695	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4075696	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4243478	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4280983	0.92[EUR][1000 genomes]
rs4314514	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4316025	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4360151	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4391282	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4435956	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4566902	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4896852	0.92[EUR][1000 genomes]
rs6570736	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6570738	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6908063	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6910790	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6913797	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6914813	0.90[EUR][1000 genomes]
rs6917482	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6922507	0.91[EUR][1000 genomes]
rs6923545	0.90[EUR][1000 genomes]
rs6924159	0.91[EUR][1000 genomes]
rs6926076	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6926657	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6930975	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6934467	0.87[EUR][1000 genomes]
rs6938972	0.87[EUR][1000 genomes]
rs7739418	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7747576	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7753092	0.90[EUR][1000 genomes]
rs7753696	0.92[EUR][1000 genomes]
rs7755440	0.91[EUR][1000 genomes]
rs854145	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs864390	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs866473	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9322043	0.93[EUR][1000 genomes]
rs9322046	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322047	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9322048	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs932522	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9373485	0.88[EUR][1000 genomes]
rs9376968	0.81[ASN][1000 genomes]
rs9376970	0.90[EUR][1000 genomes]
rs9376971	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9376975	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9386141	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9390365	0.89[EUR][1000 genomes]
rs9390377	0.91[EUR][1000 genomes]
rs9399569	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9399571	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9399573	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9403755	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403756	0.91[EUR][1000 genomes]
rs9403757	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9403764	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9403765	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9403767	0.87[EUR][1000 genomes]
rs9403768	0.87[EUR][1000 genomes]
rs9497424	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9497425	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9497427	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9497431	0.89[EUR][1000 genomes]
rs9497434	0.91[EUR][1000 genomes]
rs9497435	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs969694	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9791313	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034226	chr6:146071068-146306942	Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv830835	chr6:146145148-146287473	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56181683	RP11-545I5.3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:146286200-146287000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
2	chr6:146286200-146287400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
3	chr6:146286400-146286800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr6:146286400-146286800	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr6:146286400-146286800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr6:146286400-146287000	Enhancers	Primary B cells from peripheral blood	blood
7	chr6:146286400-146287000	Enhancers	Primary T helper naive cells from peripheral blood	blood
8	chr6:146286400-146287000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr6:146286400-146287000	Enhancers	Primary T killer memory cells from peripheral blood	blood
10	chr6:146286400-146287000	Enhancers	Brain Cingulate Gyrus	brain
11	chr6:146286400-146287000	Enhancers	Brain Hippocampus Middle	brain
12	chr6:146286400-146287200	Enhancers	Primary T helper cells PMA-I stimulated	--
13	chr6:146286400-146287400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:146286400-146287600	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr6:146286600-146286800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr6:146286600-146287000	Active TSS	Colon Smooth Muscle	Colon
17	chr6:146286600-146287200	Enhancers	Dnd41	blood
18	chr6:146286600-146287400	Enhancers	K562	blood

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