Variant report

Variant	rs13414850
Chromosome Location	chr2:187094545-187094546
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 62 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10177153	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10178888	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10196955	0.89[ASN][1000 genomes]
rs10200749	0.85[ASN][1000 genomes]
rs10208643	0.89[ASN][1000 genomes]
rs1037241	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10931240	0.82[AMR][1000 genomes]
rs11675633	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11680486	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688988	0.89[ASN][1000 genomes]
rs11692028	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11693797	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11895483	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11898666	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11901465	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12328822	0.89[ASN][1000 genomes]
rs13393891	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13397188	0.89[ASN][1000 genomes]
rs13428033	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1448855	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1868383	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2044683	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2084488	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2084489	0.89[ASN][1000 genomes]
rs2084490	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2370688	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2887826	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35642346	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55719959	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56137171	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61226319	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61434493	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6434167	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6434174	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6715493	0.81[AMR][1000 genomes]
rs6716324	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6717525	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6721789	0.89[ASN][1000 genomes]
rs6728382	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6731567	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72893450	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72895449	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72899852	0.87[EUR][1000 genomes]
rs72905615	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7579259	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7582412	0.81[AMR][1000 genomes]
rs7585889	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7588607	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7597954	0.89[ASN][1000 genomes]
rs7606920	0.80[AMR][1000 genomes]
rs9288129	0.89[ASN][1000 genomes]
rs9917285	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv875545	chr2:186566024-187280164	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv817325	chr2:186625679-187200841	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv868949	chr2:186657142-187327560	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv1002243	chr2:186692815-187150225	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv536077	chr2:186692815-187150225	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv932296	chr2:186737443-187265790	Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv875548	chr2:186798249-187164657	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1003369	chr2:186980675-187133740	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
9	nsv1014726	chr2:187036909-187213113	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv536078	chr2:187036909-187213113	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13414850	ZC3H15	Cis_1M	lymphoblastoid	RTeQTL
rs13414850	ITGAV	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187091800-187105400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:187093400-187094800	ZNF genes & repeats	Liver	Liver
3	chr2:187093400-187095000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr2:187093400-187095200	ZNF genes & repeats	Ovary	ovary
5	chr2:187093600-187094800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:187093600-187095200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
7	chr2:187093600-187095600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:187093600-187095600	ZNF genes & repeats	Fetal Intestine Small	intestine
9	chr2:187094000-187095000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr2:187094000-187095200	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
11	chr2:187094000-187095600	ZNF genes & repeats	Adipose Nuclei	Adipose
12	chr2:187094200-187095000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
13	chr2:187094200-187095600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
14	chr2:187094400-187094600	ZNF genes & repeats	Colon Smooth Muscle	Colon
15	chr2:187094400-187094800	ZNF genes & repeats	Gastric	stomach
16	chr2:187094400-187094800	ZNF genes & repeats	Left Ventricle	heart
17	chr2:187094400-187095000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr2:187094400-187095000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr2:187094400-187095000	ZNF genes & repeats	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr2:187094400-187095000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr2:187094400-187095000	ZNF genes & repeats	Pancreas	Pancrea
22	chr2:187094400-187095200	ZNF genes & repeats	iPS-15b Cell Line	embryonic stem cell
23	chr2:187094400-187095400	ZNF genes & repeats	Aorta	Aorta
24	chr2:187094400-187095600	ZNF genes & repeats	Fetal Stomach	stomach

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