Variant report

Variant	rs6856137
Chromosome Location	chr4:142160161-142160162
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:142150077..142152832-chr4:142160080..142162137,2	K562	blood:
2	chr4:142142186..142143758-chr4:142159859..142162122,2	K562	blood:
3	chr4:142157764..142162103-chr4:142246811..142251901,4	K562	blood:

Variant related genes	Relation type
ENSG00000248810	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11100712	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11100713	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11934874	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12646903	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12649778	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1435129	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1435134	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1550057	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17007017	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17007038	1.00[CEU][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17350440	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34402449	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3733484	0.91[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3756106	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3775594	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4956527	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4956528	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4956529	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58253388	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs59162293	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62327562	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62327564	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62327566	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62327586	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6851044	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6855774	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs715378	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7663811	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7679975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7684664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7697238	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7698661	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9637655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757959	chr4:142065661-142367951	Enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv2759287	chr4:142065661-142367951	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6856137	ZNF330	cis	multi-tissue	Pritchard
rs6856137	ZNF330	cis	lymphoblastoid	seeQTL
rs6856137	ZNF330	cis	cerebellum	SCAN
rs6856137	PTK2	trans	lymphoblastoid	seeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142151400-142166600	Weak transcription	NHLF	lung
2	chr4:142155200-142160200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr4:142155400-142160400	Weak transcription	Fetal Lung	lung
4	chr4:142155400-142167400	Weak transcription	K562	blood
5	chr4:142156000-142166800	Weak transcription	NHDF-Ad	bronchial
6	chr4:142156600-142163200	Weak transcription	Brain Hippocampus Middle	brain
7	chr4:142156600-142166600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr4:142156600-142166800	Weak transcription	NH-A	brain
9	chr4:142156800-142161600	Weak transcription	Gastric	stomach
10	chr4:142156800-142166600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr4:142156800-142166600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr4:142156800-142166600	Weak transcription	Osteobl	bone
13	chr4:142156800-142166800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr4:142156800-142167400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr4:142157000-142161600	Weak transcription	GM12878-XiMat	blood
16	chr4:142157000-142166600	Weak transcription	HSMMtube	muscle
17	chr4:142157000-142167000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr4:142157200-142160600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr4:142157200-142166600	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr4:142157200-142167000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr4:142157200-142167000	Weak transcription	Adipose Nuclei	Adipose
22	chr4:142157200-142167200	Weak transcription	Fetal Heart	heart
23	chr4:142157200-142167400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr4:142157400-142160200	Weak transcription	Left Ventricle	heart
25	chr4:142157600-142160400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr4:142158000-142161200	Weak transcription	Primary T cells from cord blood	blood
27	chr4:142158000-142166600	Weak transcription	HSMM	muscle

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