Variant report

Variant	rs9090
Chromosome Location	chr4:75972413-75972414
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:75969330..75970908-chr4:75971983..75973843,2	K562	blood:
2	chr4:75967944..75969741-chr4:75971903..75973478,2	MCF-7	breast:
3	chr4:75970596..75973286-chr4:75981440..75983970,2	MCF-7	breast:
4	chr4:75971065..75972930-chr4:75979010..75980545,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10007853	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10012438	0.94[ASW][hapmap];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];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10015360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10015456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10018358	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1043634	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518133	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11943279	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1346138	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16997586	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs17000108	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17000109	1.00[CHB][hapmap];0.85[JPT][hapmap];0.92[ASN][1000 genomes]
rs17000112	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17000114	0.94[ASN][1000 genomes]
rs17000141	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000149	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17198085	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17250403	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17250773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28461358	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3733466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3733467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3775530	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs3796683	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6824037	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6829853	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6836425	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6838268	1.00[MEX][hapmap]
rs6851144	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660383	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72660386	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs72660401	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7654416	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7680016	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7683115	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs890289	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1005324	chr4:75689880-76233555	Bivalent/Poised TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv537142	chr4:75689880-76233555	Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9090	DKFZP564O0823	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75940000-75976200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:75956400-75976000	Weak transcription	Spleen	Spleen
3	chr4:75956800-75982800	Weak transcription	Pancreas	Pancrea
4	chr4:75957200-75976400	Weak transcription	Colonic Mucosa	Colon
5	chr4:75962800-75975800	Weak transcription	Fetal Intestine Large	intestine
6	chr4:75963200-75976000	Weak transcription	Adipose Nuclei	Adipose
7	chr4:75967800-75974800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:75971000-75972800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:75971000-75974000	Enhancers	Fetal Heart	heart
10	chr4:75971000-75974800	Strong transcription	Aorta	Aorta
11	chr4:75971200-75974000	Strong transcription	Rectal Mucosa Donor 29	rectum
12	chr4:75971200-75974800	Strong transcription	Fetal Muscle Leg	muscle
13	chr4:75971800-75972800	Weak transcription	Right Atrium	heart
14	chr4:75971800-75976600	Weak transcription	Left Ventricle	heart
15	chr4:75971800-75978600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:75971800-75979200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:75972200-75973600	Weak transcription	Fetal Muscle Trunk	muscle
18	chr4:75972200-75976600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr4:75972400-75973000	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr4:75972400-75973600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr4:75972400-75975800	Weak transcription	Primary B cells from peripheral blood	blood
22	chr4:75972400-75975800	Weak transcription	Fetal Intestine Small	intestine

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