Variant report

Variant	rs7654416
Chromosome Location	chr4:75942683-75942684
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:75940610..75943355-chr4:75943789..75945770,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10007853	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10012438	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];0.89[ASN][1000 genomes]
rs10015360	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10015456	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs10018358	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1043633	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1043634	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10518133	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11943279	0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1346138	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16997586	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17000108	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000109	0.85[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17000112	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000114	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000141	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17000149	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17000150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17198085	0.89[AMR][1000 genomes]
rs17250403	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17250773	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs28461358	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28582004	0.98[EUR][1000 genomes]
rs3733466	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3733467	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3775530	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796683	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6824037	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6829853	1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6836425	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6838268	1.00[MEX][hapmap]
rs6851144	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72660383	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660386	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72660401	0.89[AMR][1000 genomes]
rs7680016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7683115	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs890289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9090	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]

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
rs7654416	DKFZP564O0823	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75930400-75953000	Weak transcription	Right Atrium	heart
2	chr4:75931200-75945800	Weak transcription	Gastric	stomach
3	chr4:75937000-75943200	Weak transcription	Fetal Kidney	kidney
4	chr4:75938400-75944400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:75938400-75952800	Weak transcription	Brain Anterior Caudate	brain
6	chr4:75938800-75943200	Weak transcription	Colonic Mucosa	Colon
7	chr4:75938800-75962000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr4:75939000-75945400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr4:75939000-75950400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr4:75939800-75945600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr4:75939800-75952200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr4:75940000-75943800	Weak transcription	Fetal Muscle Trunk	muscle
13	chr4:75940000-75949800	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr4:75940000-75976200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr4:75940200-75948800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr4:75940200-75953000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr4:75940400-75949200	Weak transcription	Fetal Intestine Small	intestine
18	chr4:75941000-75959000	Weak transcription	Aorta	Aorta
19	chr4:75941600-75942800	Enhancers	Left Ventricle	heart
20	chr4:75941600-75945600	Weak transcription	Fetal Intestine Large	intestine
21	chr4:75942000-75942800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr4:75942000-75943600	Enhancers	Fetal Heart	heart
23	chr4:75942000-75950000	Weak transcription	Pancreas	Pancrea
24	chr4:75942000-75956000	Weak transcription	Adipose Nuclei	Adipose
25	chr4:75942200-75949600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr4:75942600-75942800	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr4:75942600-75943600	Weak transcription	Fetal Muscle Leg	muscle
28	chr4:75942600-75950000	Weak transcription	Right Ventricle	heart

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