Variant report

Variant	rs1003908
Chromosome Location	chr4:111004666-111004667
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10005776	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10024683	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11731407	0.96[CEU][hapmap];0.86[GIH][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes]
rs2005701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2040710	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2347600	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2347601	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2347602	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28694077	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28706838	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28712862	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28784911	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34392886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4698807	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6858635	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6858695	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869392	chr4:110945459-111235071	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv437412	chr4:110995217-111006785	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
3	nsv437414	chr4:110995217-111006785	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS	n/a	n/a	inside rSNPs	diseases
4	esv2760833	chr4:111003987-111005006	Weak transcription ZNF genes & repeats Strong transcription Enhancers	n/a	n/a	inside rSNPs	diseases
5	esv14346	chr4:111004040-111004990	Weak transcription Strong transcription ZNF genes & repeats Enhancers	n/a	n/a	inside rSNPs	diseases
6	esv3341709	chr4:111004303-111006876	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:110973000-111009200	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr4:110981400-111006200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr4:110981400-111009200	Weak transcription	Primary hematopoietic stem cells	blood
4	chr4:110984000-111006200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr4:110985600-111006000	Weak transcription	Fetal Intestine Small	intestine
6	chr4:110986200-111009400	Weak transcription	NHLF	lung
7	chr4:110986800-111006000	Weak transcription	HepG2	liver
8	chr4:110990400-111006400	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr4:110991800-111008400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr4:110992400-111010000	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr4:110993200-111015400	Weak transcription	Psoas Muscle	Psoas
12	chr4:110994800-111006000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr4:110995000-111018600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr4:110995200-111008600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr4:110996400-111006200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:110998000-111006000	Weak transcription	K562	blood
17	chr4:110998200-111007800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr4:111003400-111006000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr4:111004000-111004800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr4:111004000-111004800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr4:111004000-111004800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:111004000-111005000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:111004200-111004800	Strong transcription	NHEK	skin
24	chr4:111004200-111005000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr4:111004400-111009600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr4:111004400-111009600	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr4:111004600-111005800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr4:111004600-111006000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr4:111004600-111006000	Weak transcription	Small Intestine	intestine
30	chr4:111004600-111006000	Weak transcription	Dnd41	blood
31	chr4:111004600-111007000	Weak transcription	Brain Germinal Matrix	brain
32	chr4:111004600-111026000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr4:111004600-111027800	Weak transcription	Esophagus	oesophagus

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