Variant report

Variant	rs2972393
Chromosome Location	chr5:42496257-42496258
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	chr5:42493810..42496602-chr5:42496863..42498426,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10941577	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11739243	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11741390	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748084	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12514403	0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13153388	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13166255	0.92[ASN][1000 genomes]
rs13166285	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13169289	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13178282	0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13178652	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13189275	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1509460	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap]
rs1509462	0.82[CHB][hapmap];0.85[JPT][hapmap];0.95[ASN][1000 genomes]
rs1509463	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2089645	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28943875	0.95[ASN][1000 genomes]
rs2940913	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2940923	0.85[CEU][hapmap]
rs2940937	0.98[ASN][1000 genomes]
rs2940944	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.99[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972408	0.85[CEU][hapmap]
rs2972418	0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[MKK][hapmap];0.98[ASN][1000 genomes]
rs2972420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs33956936	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35500216	0.98[ASN][1000 genomes]
rs4130114	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509029	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530764	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866790	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4866931	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866932	0.95[ASN][1000 genomes]
rs4866933	0.95[ASN][1000 genomes]
rs4866934	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4866935	0.92[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs58179197	0.95[ASN][1000 genomes]
rs6451621	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6451622	0.86[ASN][1000 genomes]
rs6451624	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[MKK][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6897318	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7705834	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7710528	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7721578	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723304	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933208	chr5:41879946-42876624	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	112 gene(s)	inside rSNPs	diseases
2	nsv492147	chr5:41902086-42896162	Enhancers Flanking Active TSS Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	113 gene(s)	inside rSNPs	diseases
3	nsv948514	chr5:42270161-42519262	Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1020464	chr5:42488628-42699394	Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv1018751	chr5:42491883-42697923	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972393	HCN1	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:42490600-42499200	Weak transcription	Pancreas	Pancrea
2	chr5:42490800-42499200	Weak transcription	Left Ventricle	heart
3	chr5:42491800-42496400	Weak transcription	Stomach Smooth Muscle	stomach
4	chr5:42492000-42499200	Weak transcription	Right Atrium	heart
5	chr5:42492200-42496600	Weak transcription	Liver	Liver
6	chr5:42492200-42499200	Weak transcription	Fetal Muscle Leg	muscle
7	chr5:42492200-42499200	Weak transcription	Ovary	ovary
8	chr5:42493200-42499800	Weak transcription	Fetal Lung	lung
9	chr5:42494000-42498400	Enhancers	Fetal Heart	heart
10	chr5:42494200-42496600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:42494200-42496800	Enhancers	NHEK	skin
12	chr5:42494400-42496800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:42494600-42496400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr5:42494600-42499000	Weak transcription	Adipose Nuclei	Adipose
15	chr5:42494800-42497200	Enhancers	Colon Smooth Muscle	Colon
16	chr5:42495200-42497000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr5:42495200-42500000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr5:42495400-42497600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:42495800-42496400	Enhancers	HSMMtube	muscle
20	chr5:42495800-42496600	Enhancers	Rectal Smooth Muscle	rectum
21	chr5:42495800-42496800	Enhancers	HMEC	breast
22	chr5:42495800-42497200	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr5:42495800-42497600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr5:42495800-42499200	Weak transcription	Right Ventricle	heart
25	chr5:42496000-42496600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr5:42496000-42498400	Enhancers	Psoas Muscle	Psoas
27	chr5:42496000-42501200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr5:42496200-42496400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:42496200-42496600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr5:42496200-42498600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr5:42496200-42499000	Enhancers	iPS-15b Cell Line	embryonic stem cell

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