Variant report

Variant	rs2346177
Chromosome Location	chr2:46642249-46642250
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	chr2:46640448..46643419-chr2:46661889..46663890,2	K562	blood:
2	chr2:46639689..46643864-chr2:46655202..46657134,3	K562	blood:

Variant related genes	Relation type
ENSG00000187600	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11125074	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11125075	0.84[CEU][hapmap];0.85[TSI][hapmap]
rs12619985	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12986585	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12991646	0.81[EUR][1000 genomes]
rs12994892	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13010062	0.81[EUR][1000 genomes]
rs1447563	0.84[CEU][hapmap]
rs1447565	0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1530625	0.91[GIH][hapmap];0.82[ASN][1000 genomes]
rs1530627	0.91[GIH][hapmap];0.80[ASN][1000 genomes]
rs1530628	0.83[CHB][hapmap];0.93[GIH][hapmap];0.87[MEX][hapmap];0.80[ASN][1000 genomes]
rs1597041	0.81[ASN][1000 genomes]
rs1868096	0.80[ASN][1000 genomes]
rs2166745	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2197698	0.80[ASN][1000 genomes]
rs2346178	0.86[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2881327	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34186951	0.82[ASN][1000 genomes]
rs4413204	0.86[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4953365	0.82[EUR][1000 genomes]
rs4953372	0.88[CEU][hapmap]
rs4953373	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4953374	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62138876	0.93[ASN][1000 genomes]
rs6726089	0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6737959	0.89[GIH][hapmap]
rs7556828	0.91[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap]
rs7559484	0.95[GIH][hapmap];0.83[ASN][1000 genomes]
rs7571742	0.93[GIH][hapmap];0.83[ASN][1000 genomes]
rs7587138	0.95[GIH][hapmap];0.83[MEX][hapmap]
rs7598507	0.83[ASN][1000 genomes]
rs7598584	0.83[ASN][1000 genomes]
rs7598712	0.83[ASN][1000 genomes]

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	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	nsv457330	chr2:46637081-46660752	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv581744	chr2:46637081-46660752	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
HDL cholesterol	21347282	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2346177	ATP6V1E2	cis	parietal	SCAN
rs2346177	CRIPT	cis	lymphoblastoid	seeQTL
rs2346177	PIGF	cis	cerebellum	SCAN
rs2346177	CRIPT	cis	multi-tissue	Pritchard

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46613200-46644200	Weak transcription	Aorta	Aorta
2	chr2:46636800-46646200	Weak transcription	K562	blood
3	chr2:46637200-46642600	Enhancers	HepG2	liver
4	chr2:46639400-46643800	Weak transcription	Hela-S3	cervix
5	chr2:46642000-46644000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr2:46642200-46644200	Weak transcription	Placenta	Placenta
7	chr2:46642200-46645600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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