Variant report

Variant	rs12144282
Chromosome Location	chr1:62701741-62701742
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1050334	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10789108	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs10889309	0.99[ASN][1000 genomes]
rs10889310	0.87[ASN][1000 genomes]
rs10889313	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10889315	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11207941	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11207942	0.93[ASN][1000 genomes]
rs11207943	0.99[ASN][1000 genomes]
rs11207944	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11207945	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11207946	0.99[ASN][1000 genomes]
rs11207947	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11207948	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12030846	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12089897	0.99[ASN][1000 genomes]
rs12096118	0.86[ASN][1000 genomes]
rs12120789	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12131947	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12138777	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2067994	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2457812	0.86[ASN][1000 genomes]
rs2481689	0.85[ASN][1000 genomes]
rs2666478	0.82[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs2774928	0.99[ASN][1000 genomes]
rs41289438	1.00[ASN][1000 genomes]
rs4322258	0.91[CEU][hapmap];0.92[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55673263	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs56318037	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs59025845	0.82[EUR][1000 genomes]
rs61775734	1.00[ASN][1000 genomes]
rs61775736	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61775737	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660963	0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6664672	0.92[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6671554	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6680953	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688986	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696307	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6696486	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7553446	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004446	chr1:62394631-62813533	Enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534984	chr1:62394631-62813533	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1009398	chr1:62656660-62780644	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12144282	KANK4	cis	parietal	SCAN

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:62695800-62703400	Weak transcription	Adipose Nuclei	Adipose
2	chr1:62696600-62703600	Weak transcription	Fetal Stomach	stomach
3	chr1:62697000-62702800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr1:62697000-62703600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr1:62697000-62706600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:62697200-62702800	Weak transcription	A549	lung
7	chr1:62697400-62701800	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr1:62697400-62702400	Weak transcription	NH-A	brain
9	chr1:62697400-62703200	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:62698200-62704000	Enhancers	NHEK	skin
11	chr1:62698600-62704400	Enhancers	Hela-S3	cervix
12	chr1:62699000-62702800	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr1:62699000-62706600	Weak transcription	Fetal Lung	lung
14	chr1:62699000-62706800	Weak transcription	Pancreas	Pancrea
15	chr1:62699200-62703600	Weak transcription	Fetal Muscle Leg	muscle
16	chr1:62699800-62704200	Enhancers	HMEC	breast
17	chr1:62700000-62701800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:62700000-62702400	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr1:62700000-62702800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr1:62700000-62704000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:62700200-62703400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr1:62700400-62704000	Enhancers	HSMM	muscle
23	chr1:62700600-62703400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:62700800-62703400	Weak transcription	Placenta	Placenta
25	chr1:62700800-62703800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:62701000-62701800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:62701000-62702000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr1:62701000-62702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:62701000-62702800	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr1:62701000-62703000	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr1:62701000-62703400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr1:62701000-62703400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:62701000-62703600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:62701000-62707400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr1:62701000-62710800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr1:62701400-62709400	Weak transcription	Fetal Intestine Small	intestine
37	chr1:62701600-62702200	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr1:62701600-62704200	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr1:62701600-62704200	Enhancers	HSMMtube	muscle
40	chr1:62701600-62705000	Enhancers	HepG2	liver

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