Variant report

Variant	rs12602058
Chromosome Location	chr17:20897623-20897624
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:20895064..20900549-chr17:20901410..20906180,6	K562	blood:
2	chr17:20895463..20898047-chr17:20898321..20900254,2	K562	blood:
3	chr17:20896404..20898523-chr17:20904680..20906876,2	K562	blood:

Variant related genes	Relation type
ENSG00000263986	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1045162	0.84[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.91[TSI][hapmap];0.95[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1127814	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11867648	0.89[MKK][hapmap]
rs12051606	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12600703	0.84[CEU][hapmap];0.90[JPT][hapmap];0.82[MKK][hapmap];0.86[AMR][1000 genomes]
rs12601292	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12946114	0.81[ASN][1000 genomes]
rs1531566	0.83[ASN][1000 genomes]
rs1542552	1.00[ASW][hapmap];0.94[CEU][hapmap];0.81[CHB][hapmap];0.84[CHD][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17770614	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2054464	0.93[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2127095	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2291034	0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2364326	0.84[CEU][hapmap];0.94[CHB][hapmap];0.89[JPT][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2886105	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4445951	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4985811	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4985814	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985815	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4985816	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4985959	0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs4985963	0.89[CHD][hapmap];0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs4985966	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4985968	0.89[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4985969	0.84[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];1.00[MKK][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4985970	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4985971	0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4985975	0.86[AMR][1000 genomes]
rs56209912	0.83[ASN][1000 genomes]
rs56323013	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58235085	0.92[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs59543297	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs59713572	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6618	0.87[ASN][1000 genomes]
rs719093	0.84[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.95[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7209129	0.89[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7216921	0.85[ASN][1000 genomes]
rs880653	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs899337	0.94[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs899340	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs9911289	0.89[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2751619	chr17:20462908-20914156	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv949097	chr17:20801739-21406355	Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	nsv529759	chr17:20839079-21529632	Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
4	nsv827917	chr17:20896100-20961777	Flanking Active TSS Enhancers Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12602058	RP11-344E13.3	cis	Artery Tibial	GTEx
rs12602058	RP11-344E13.3	cis	Nerve Tibial	GTEx
rs12602058	RP11-344E13.3	cis	Heart Left Ventricle	GTEx
rs12602058	RP11-344E13.3	cis	Stomach	GTEx
rs12602058	RP11-344E13.3	cis	Whole Blood	GTEx
rs12602058	RP11-344E13.3	cis	Esophagus Mucosa	GTEx
rs12602058	RP11-344E13.3	cis	Adipose Subcutaneous	GTEx
rs12602058	RP11-344E13.3	cis	Skin Sun Exposed Lower leg	GTEx
rs12602058	RP11-344E13.3	cis	lung	GTEx
rs12602058	RP11-344E13.3	cis	Esophagus Muscularis	GTEx
rs12602058	RP11-344E13.3	cis	Muscle Skeletal	GTEx
rs12602058	RP11-344E13.3	cis	Thyroid	GTEx
rs12602058	GRAP	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:20893000-20901600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr17:20893800-20901200	Weak transcription	Right Atrium	heart
3	chr17:20894800-20899000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr17:20895800-20898000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr17:20896200-20898000	Enhancers	Hela-S3	cervix
6	chr17:20896400-20898000	Enhancers	Rectal Mucosa Donor 31	rectum
7	chr17:20896400-20898400	Enhancers	Stomach Mucosa	stomach
8	chr17:20896400-20900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:20896400-20901400	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr17:20896400-20901600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr17:20896400-20902800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr17:20896600-20898200	Enhancers	Spleen	Spleen
13	chr17:20896600-20901800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr17:20896600-20901800	Weak transcription	HUVEC	blood vessel
15	chr17:20896600-20902000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr17:20896600-20906800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr17:20896800-20899400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr17:20896800-20899400	Weak transcription	Right Ventricle	heart
19	chr17:20896800-20899600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr17:20896800-20900000	Weak transcription	Adipose Nuclei	Adipose
21	chr17:20896800-20900000	Weak transcription	Fetal Muscle Leg	muscle
22	chr17:20896800-20900600	Weak transcription	Esophagus	oesophagus
23	chr17:20896800-20900600	Weak transcription	Fetal Intestine Small	intestine
24	chr17:20896800-20900600	Weak transcription	Left Ventricle	heart
25	chr17:20896800-20900800	Weak transcription	Brain Germinal Matrix	brain
26	chr17:20896800-20900800	Weak transcription	Fetal Brain Female	brain
27	chr17:20896800-20901000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr17:20896800-20901000	Weak transcription	Ovary	ovary
29	chr17:20896800-20901400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr17:20896800-20901400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr17:20896800-20901400	Weak transcription	Fetal Lung	lung
32	chr17:20896800-20901600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr17:20896800-20901600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr17:20896800-20901600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr17:20896800-20901600	Weak transcription	HSMM	muscle
36	chr17:20896800-20901800	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr17:20896800-20901800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr17:20896800-20901800	Weak transcription	NHDF-Ad	bronchial
39	chr17:20896800-20902200	Weak transcription	Primary B cells from peripheral blood	blood
40	chr17:20896800-20902200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr17:20896800-20902200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr17:20896800-20902200	Weak transcription	Fetal Thymus	thymus
43	chr17:20896800-20902400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr17:20896800-20902600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr17:20896800-20902600	Weak transcription	Colonic Mucosa	Colon
46	chr17:20896800-20902600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr17:20896800-20902600	Weak transcription	NHEK	skin
48	chr17:20896800-20904200	Weak transcription	Primary T cells from cord blood	blood
49	chr17:20896800-20904800	Weak transcription	Fetal Kidney	kidney
50	chr17:20896800-20905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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