Variant report

Variant	rs1346138
Chromosome Location	chr4:75958211-75958212
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10007853	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10012438	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10015360	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10015456	0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10018358	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1043633	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1043634	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10518133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11943279	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16997586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000108	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000109	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17000112	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000114	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17000141	0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17000149	0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17000150	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs17196260	0.87[CEU][hapmap]
rs17198085	0.92[AMR][1000 genomes]
rs17249558	0.85[CEU][hapmap]
rs17250403	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17250773	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17386703	0.87[CEU][hapmap]
rs28461358	0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28582004	0.95[EUR][1000 genomes]
rs3733466	0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3733467	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3775530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3796683	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6824037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6829853	1.00[CHB][hapmap];0.82[JPT][hapmap];0.96[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6836425	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6838268	0.82[CEU][hapmap]
rs6851144	0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72660383	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72660386	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72660401	0.92[AMR][1000 genomes]
rs7654416	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]
rs7680016	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7683115	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs890289	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs9090	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[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
rs1346138	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	chr4:75941000-75959000	Weak transcription	Aorta	Aorta
4	chr4:75942800-75962200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:75944200-75971000	Weak transcription	Fetal Muscle Trunk	muscle
6	chr4:75949800-75963600	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr4:75951800-75965200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr4:75954400-75959000	Weak transcription	Fetal Muscle Leg	muscle
9	chr4:75954400-75971000	Weak transcription	Fetal Heart	heart
10	chr4:75956400-75960000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr4:75956400-75962400	Weak transcription	Left Ventricle	heart
12	chr4:75956400-75976000	Weak transcription	Spleen	Spleen
13	chr4:75956600-75959000	Weak transcription	Lung	lung
14	chr4:75956600-75960000	Weak transcription	Adipose Nuclei	Adipose
15	chr4:75956600-75961000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr4:75956600-75964800	Weak transcription	Stomach Mucosa	stomach
17	chr4:75956800-75959200	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr4:75956800-75960000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr4:75956800-75967600	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:75956800-75982800	Weak transcription	Pancreas	Pancrea
21	chr4:75957000-75959800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr4:75957000-75959800	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr4:75957200-75976400	Weak transcription	Colonic Mucosa	Colon
24	chr4:75957600-75959000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr4:75957600-75962200	Weak transcription	Fetal Intestine Large	intestine
26	chr4:75957600-75971200	Weak transcription	Fetal Intestine Small	intestine
27	chr4:75958000-75959000	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr4:75958200-75960000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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