Variant report

Variant	rs17000112
Chromosome Location	chr4:75959505-75959506
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10007853	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10012438	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10015360	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10015456	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs10018358	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1043633	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1043634	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10518133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11943279	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1346138	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16997586	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000108	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000109	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000114	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000141	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17000149	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17000150	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17198085	0.92[AMR][1000 genomes]
rs17250403	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17250773	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs28461358	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28582004	0.95[EUR][1000 genomes]
rs3733466	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3733467	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3775530	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3796683	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6824037	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6829853	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6836425	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6851144	0.96[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs72660383	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72660386	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660401	0.92[AMR][1000 genomes]
rs7654416	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7680016	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7683115	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs890289	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9090	0.86[AMR][1000 genomes];0.94[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
rs17000112	DKFZP564O0823	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75938800-75962000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr4:75940000-75976200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:75942800-75962200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr4:75944200-75971000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr4:75949800-75963600	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr4:75951800-75965200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr4:75954400-75971000	Weak transcription	Fetal Heart	heart
8	chr4:75956400-75960000	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr4:75956400-75962400	Weak transcription	Left Ventricle	heart
10	chr4:75956400-75976000	Weak transcription	Spleen	Spleen
11	chr4:75956600-75960000	Weak transcription	Adipose Nuclei	Adipose
12	chr4:75956600-75961000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr4:75956600-75964800	Weak transcription	Stomach Mucosa	stomach
14	chr4:75956800-75960000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr4:75956800-75967600	Weak transcription	Colon Smooth Muscle	Colon
16	chr4:75956800-75982800	Weak transcription	Pancreas	Pancrea
17	chr4:75957000-75959800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr4:75957000-75959800	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr4:75957200-75976400	Weak transcription	Colonic Mucosa	Colon
20	chr4:75957600-75962200	Weak transcription	Fetal Intestine Large	intestine
21	chr4:75957600-75971200	Weak transcription	Fetal Intestine Small	intestine
22	chr4:75958200-75960000	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:75959000-75960800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr4:75959000-75961000	Genic enhancers	Rectal Mucosa Donor 31	rectum
25	chr4:75959000-75961600	Strong transcription	Fetal Muscle Leg	muscle
26	chr4:75959000-75963000	Strong transcription	Aorta	Aorta
27	chr4:75959200-75960600	Genic enhancers	Rectal Mucosa Donor 29	rectum
28	chr4:75959400-75960400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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