Variant report

Variant	rs7562332
Chromosome Location	chr2:46710405-46710406
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46709342..46712080-chr2:46908104..46909816,2	K562	blood:
2	chr2:46707494..46710484-chr2:46718946..46721502,2	K562	blood:
3	chr2:46710065..46711846-chr2:46725513..46727572,2	MCF-7	breast:
4	chr2:46710349..46713099-chr2:46769270..46771905,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction
ENSG00000253515	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11125074	0.82[ASN][1000 genomes]
rs11125077	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12473626	0.96[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12619420	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13009087	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13017856	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13018019	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13018477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13025174	0.96[CEU][hapmap];0.86[CHB][hapmap];0.94[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13025967	0.86[EUR][1000 genomes]
rs13032473	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13033917	0.96[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1530625	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530627	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1530628	0.80[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.80[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1542271	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1597041	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1823561	0.84[ASN][1000 genomes]
rs1868080	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1868096	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2053765	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2084345	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2121697	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2121700	0.84[CEU][hapmap]
rs2197698	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2276555	0.82[ASW][hapmap];0.96[CEU][hapmap];0.81[CHD][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2346178	0.82[CHB][hapmap]
rs34186951	0.81[ASN][1000 genomes]
rs3814047	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3814048	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3863000	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4366955	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4456747	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4952827	0.82[CHB][hapmap]
rs4953377	0.84[EUR][1000 genomes]
rs4953381	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953384	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4953385	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4953389	0.96[CEU][hapmap];0.88[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6544894	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6715279	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6728611	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6728847	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6737959	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7556828	0.95[CHB][hapmap];0.86[GIH][hapmap];0.83[EUR][1000 genomes]
rs7557998	0.88[CEU][hapmap];0.88[CHD][hapmap];0.85[GIH][hapmap];0.89[JPT][hapmap];0.88[MEX][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7559484	0.88[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7565770	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7565850	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7571742	0.88[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.80[GIH][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7587138	0.91[CHB][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap];0.80[TSI][hapmap]
rs7588586	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7588938	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598507	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7598584	0.88[CEU][hapmap];0.91[CHB][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7598712	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv581746	chr2:46699145-46719922	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
15	nsv581747	chr2:46709571-46718989	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	esv33715	chr2:46709764-46712792	Weak transcription Enhancers Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7562332	CRIPT	cis	parietal	SCAN
rs7562332	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46689200-46714800	Weak transcription	Right Atrium	heart
2	chr2:46700200-46714800	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr2:46705000-46716600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:46708400-46714800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr2:46708400-46714800	Weak transcription	Lung	lung
6	chr2:46709000-46713000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr2:46709200-46714600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:46709200-46714800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr2:46709400-46714600	Weak transcription	NHDF-Ad	bronchial
10	chr2:46709600-46714600	Weak transcription	HUVEC	blood vessel
11	chr2:46709600-46714600	Weak transcription	Osteobl	bone
12	chr2:46709600-46715000	Weak transcription	A549	lung
13	chr2:46710000-46713600	Weak transcription	Hela-S3	cervix
14	chr2:46710000-46714600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:46710000-46714600	Weak transcription	NHLF	lung
16	chr2:46710400-46710800	Enhancers	Left Ventricle	heart

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