Variant report

Variant	rs17131699
Chromosome Location	chr1:93598114-93598115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93597833..93599532-chr1:93699418..93701453,2	K562	blood:
2	chr1:93543048..93545567-chr1:93596297..93598631,2	K562	blood:
3	chr1:93579998..93581880-chr1:93596682..93599849,3	K562	blood:
4	chr1:93543048..93546270-chr1:93596297..93598631,3	K562	blood:
5	chr1:93596596..93599097-chr1:93600778..93604070,3	K562	blood:

Variant related genes	Relation type
ENSG00000143033	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10874767	0.96[TSI][hapmap]
rs11164874	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11164878	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11164882	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11586323	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12057476	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12064785	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12066315	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12067005	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12085959	0.91[CEU][hapmap]
rs12087466	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12088338	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12094547	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1414367	1.00[ASW][hapmap];0.83[LWK][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2391227	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2484485	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2749735	0.92[EUR][1000 genomes]
rs2783492	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2783498	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2783506	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2815408	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2815409	1.00[ASW][hapmap];0.83[LWK][hapmap];0.86[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2815410	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2815411	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2815412	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2815413	0.84[EUR][1000 genomes]
rs2815414	0.84[EUR][1000 genomes]
rs36057148	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4847409	0.96[TSI][hapmap]
rs504810	0.91[CEU][hapmap]
rs505531	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs506556	0.96[TSI][hapmap];0.83[EUR][1000 genomes]
rs519723	0.96[TSI][hapmap]
rs522999	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs546	1.00[ASW][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55701931	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs571212	0.92[TSI][hapmap]
rs573056	0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs581825	0.83[EUR][1000 genomes]
rs615416	0.84[EUR][1000 genomes]
rs626714	0.96[TSI][hapmap]
rs633789	0.92[TSI][hapmap]
rs658877	0.84[EUR][1000 genomes]
rs6667701	0.96[TSI][hapmap]
rs667680	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs668944	0.96[TSI][hapmap]
rs6701250	0.88[MEX][hapmap];0.96[TSI][hapmap]
rs671559	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71510760	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7519163	0.96[TSI][hapmap]
rs7555292	1.00[ASW][hapmap];0.88[LWK][hapmap];0.88[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap]
rs797660	0.86[AMR][1000 genomes];0.82[EUR][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	nsv1008602	chr1:93176811-93640808	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv830614	chr1:93465978-93678700	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv830625	chr1:93566378-93735246	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs17131699	RWDD3	cis	parietal	SCAN
rs17131699	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs17131699	RP4-717I23.3	cis	Whole Blood	GTEx
rs17131699	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs17131699	RP4-717I23.3	cis	Artery Aorta	GTEx
rs17131699	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs17131699	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs17131699	TMED5	cis	cerebellum	SCAN
rs17131699	RP4-717I23.3	cis	Thyroid	GTEx
rs17131699	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs17131699	TMED5	cis	parietal	SCAN
rs17131699	F3	cis	parietal	SCAN
rs17131699	RP4-717I23.3	cis	Artery Tibial	GTEx
rs17131699	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs17131699	RP4-717I23.3	cis	lung	GTEx
rs17131699	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs17131699	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs17131699	LOC646848	cis	normal skin	skin_eQTL
rs17131699	RP4-717I23.3	cis	Stomach	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93546200-93602200	Weak transcription	Aorta	Aorta
2	chr1:93547600-93600000	Weak transcription	HSMMtube	muscle
3	chr1:93548000-93601800	Weak transcription	NHLF	lung
4	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
5	chr1:93571400-93602200	Weak transcription	Colonic Mucosa	Colon
6	chr1:93572400-93599600	Weak transcription	Spleen	Spleen
7	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
8	chr1:93573800-93609000	Strong transcription	Fetal Thymus	thymus
9	chr1:93574200-93609000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:93574600-93609000	Strong transcription	Dnd41	blood
11	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
12	chr1:93577800-93601600	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr1:93578800-93613600	Weak transcription	Psoas Muscle	Psoas
14	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr1:93581000-93599200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr1:93581200-93616800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr1:93582400-93599800	Weak transcription	Brain Hippocampus Middle	brain
20	chr1:93582400-93600000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
22	chr1:93582400-93642800	Weak transcription	Gastric	stomach
23	chr1:93582600-93600000	Weak transcription	Ovary	ovary
24	chr1:93583000-93601400	Weak transcription	Brain Substantia Nigra	brain
25	chr1:93583000-93604200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:93583200-93602000	Weak transcription	NHDF-Ad	bronchial
27	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
28	chr1:93583600-93599600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:93583600-93599600	Weak transcription	Left Ventricle	heart
30	chr1:93583600-93600000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr1:93583600-93600800	Weak transcription	Fetal Brain Female	brain
32	chr1:93583600-93613800	Weak transcription	Lung	lung
33	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
35	chr1:93584200-93600000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:93584200-93600000	Weak transcription	Osteobl	bone
37	chr1:93584600-93600000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:93584600-93601000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:93585200-93609200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr1:93585400-93600000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr1:93585800-93601800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
43	chr1:93586200-93623400	Weak transcription	Fetal Brain Male	brain
44	chr1:93586400-93599600	Weak transcription	Fetal Muscle Trunk	muscle
45	chr1:93586400-93600000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:93586400-93600200	Weak transcription	Muscle Satellite Cultured Cells	--
47	chr1:93586400-93600200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr1:93586600-93599600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr1:93586600-93599800	Weak transcription	Brain Anterior Caudate	brain
50	chr1:93586600-93600000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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