Variant report

Variant	rs17401468
Chromosome Location	chr2:178768683-178768684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10164920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10165089	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10168605	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10170290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10170607	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs10171486	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10174604	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10181377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10182833	0.92[ASN][1000 genomes]
rs10183144	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10186239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10189134	0.85[ASW][hapmap]
rs10190066	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10190805	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10191328	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10192990	0.92[ASN][1000 genomes]
rs10193299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10194612	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10195497	0.92[ASN][1000 genomes]
rs10198681	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10198877	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs10208501	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10211341	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10221783	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];0.95[ASN][1000 genomes]
rs10497483	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10930817	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12151755	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12693128	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12693133	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12693145	0.92[ASN][1000 genomes]
rs12988331	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs12994913	1.00[CHB][hapmap]
rs12995449	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13003683	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13008170	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13008780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13009350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13015148	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs13386418	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13396207	0.92[ASN][1000 genomes]
rs13400109	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13400411	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13410185	0.88[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13411527	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13411542	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13411922	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs13411970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13413095	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13413731	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13419437	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs13422276	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13425873	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13427912	0.92[ASN][1000 genomes]
rs13428032	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs1358299	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1527291	1.00[JPT][hapmap]
rs16865818	0.82[ASN][1000 genomes]
rs16865821	0.85[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs16865846	1.00[JPT][hapmap]
rs17329742	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17329956	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17401650	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.92[ASN][1000 genomes]
rs17401671	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17401860	1.00[CHB][hapmap]
rs1898012	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs35267683	0.88[ASN][1000 genomes]
rs35385829	0.92[ASN][1000 genomes]
rs35625771	0.92[ASN][1000 genomes]
rs35758079	0.92[ASN][1000 genomes]
rs3770053	0.82[ASN][1000 genomes]
rs4377360	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4423634	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6708449	1.00[JPT][hapmap]
rs6726222	1.00[JPT][hapmap]
rs6726477	0.81[TSI][hapmap]
rs6750238	0.92[CHD][hapmap];1.00[JPT][hapmap]
rs71423515	0.92[ASN][1000 genomes]
rs71423518	0.92[ASN][1000 genomes]
rs71423519	0.92[ASN][1000 genomes]
rs7561059	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7600368	0.85[ASW][hapmap]
rs9288011	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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	nsv999086	chr2:178262348-178773585	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv536055	chr2:178262348-178773585	Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv533377	chr2:178718801-178963463	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv1007579	chr2:178729330-178890946	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv875451	chr2:178748294-178953409	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv2756313	chr2:178750158-178768683	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv998304	chr2:178756380-178924378	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv536056	chr2:178756380-178924378	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17401468	EVX2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:178762400-178770400	Weak transcription	Pancreas	Pancrea
2	chr2:178762600-178772600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:178765800-178774200	Weak transcription	HMEC	breast
4	chr2:178765800-178774600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:178766600-178772600	Weak transcription	NHEK	skin
6	chr2:178767000-178770600	Weak transcription	Liver	Liver
7	chr2:178767400-178770400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:178767800-178770600	Weak transcription	Stomach Mucosa	stomach
9	chr2:178768000-178770800	Weak transcription	Ovary	ovary
10	chr2:178768000-178773000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:178768200-178770400	Weak transcription	Adipose Nuclei	Adipose
12	chr2:178768200-178774000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:178768600-178770200	Weak transcription	Fetal Heart	heart
14	chr2:178768600-178770800	Weak transcription	Right Atrium	heart
15	chr2:178768600-178773000	Weak transcription	Left Ventricle	heart
16	chr2:178768600-178780000	Weak transcription	Psoas Muscle	Psoas

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