Variant report

Variant	rs9989017
Chromosome Location	chr12:29489564-29489565
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:29489097..29490633-chr12:29512483..29514735,2	K562	blood:
2	chr12:29487861..29489675-chr12:29532750..29535487,2	K562	blood:
3	chr12:29487854..29490275-chr12:29492417..29495567,3	K562	blood:

Variant related genes	Relation type
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10082956	0.99[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10128781	1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs1035606	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs1035607	0.87[EUR][1000 genomes]
rs10743657	0.83[AFR][1000 genomes]
rs10743658	0.83[AFR][1000 genomes]
rs10843390	1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10843391	0.85[YRI][hapmap];0.97[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs10843397	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10843398	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs10843403	0.82[AFR][1000 genomes]
rs11050175	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11050203	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11050209	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1156242	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs12320212	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12831751	0.95[YRI][hapmap];0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278093	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs2278094	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs3782513	0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3815843	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4931178	0.83[AFR][1000 genomes]
rs6487815	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7136223	0.83[AMR][1000 genomes]
rs7297435	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7311742	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7315504	0.95[YRI][hapmap];0.83[AFR][1000 genomes]
rs9651802	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs966540	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs966541	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs996498	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs9989017	RP11-996F15.2	cis	Thyroid	GTEx
rs9989017	RP11-996F15.2	cis	Stomach	GTEx
rs9989017	RP11-996F15.2	cis	Whole Blood	GTEx
rs9989017	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs9989017	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs9989017	RP11-996F15.2	cis	lung	GTEx
rs9989017	RP11-996F15.2	cis	Muscle Skeletal	GTEx
rs9989017	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs9989017	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs9989017	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs9989017	RP11-996F15.2	cis	Artery Tibial	GTEx
rs9989017	RP11-996F15.2	cis	Artery Aorta	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29452800-29494200	Weak transcription	Lung	lung
3	chr12:29459400-29493000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
5	chr12:29465000-29494200	Weak transcription	Colonic Mucosa	Colon
6	chr12:29468600-29491000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr12:29470000-29495600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:29470000-29500000	Weak transcription	K562	blood
9	chr12:29470800-29492800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr12:29470800-29492800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr12:29470800-29493400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr12:29470800-29493800	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr12:29470800-29496000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
16	chr12:29471200-29491400	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr12:29471200-29493000	Weak transcription	Brain Substantia Nigra	brain
18	chr12:29471200-29494400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:29471400-29495800	Weak transcription	Brain Anterior Caudate	brain
20	chr12:29471600-29492600	Weak transcription	Duodenum Mucosa	Duodenum
21	chr12:29472200-29493800	Weak transcription	Left Ventricle	heart
22	chr12:29473800-29493000	Weak transcription	HMEC	breast
23	chr12:29473800-29522600	Weak transcription	NHEK	skin
24	chr12:29474000-29493400	Weak transcription	HUVEC	blood vessel
25	chr12:29474200-29489600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr12:29474200-29490600	Weak transcription	NH-A	brain
27	chr12:29474200-29493000	Weak transcription	Osteobl	bone
28	chr12:29474200-29494200	Weak transcription	NHDF-Ad	bronchial
29	chr12:29474400-29490600	Weak transcription	Liver	Liver
30	chr12:29474800-29493800	Weak transcription	Fetal Intestine Large	intestine
31	chr12:29475600-29489600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:29475800-29491200	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr12:29475800-29493200	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr12:29475800-29493400	Weak transcription	Colon Smooth Muscle	Colon
35	chr12:29476000-29492200	Weak transcription	Placenta	Placenta
36	chr12:29476000-29496000	Weak transcription	Muscle Satellite Cultured Cells	--
37	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr12:29476200-29493800	Weak transcription	Fetal Muscle Trunk	muscle
39	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
40	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
42	chr12:29476400-29490800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr12:29476400-29491200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr12:29476400-29491200	Weak transcription	Fetal Thymus	thymus
45	chr12:29476400-29493000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr12:29476400-29493600	Weak transcription	Primary T cells from cord blood	blood
47	chr12:29476400-29494200	Weak transcription	Fetal Stomach	stomach
48	chr12:29476400-29498600	Weak transcription	Ovary	ovary
49	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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