Variant report

Variant	rs522999
Chromosome Location	chr1:93675100-93675101
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 151 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs1000606	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10430073	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10782958	0.83[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10874771	0.83[EUR][1000 genomes]
rs10874774	0.82[EUR][1000 genomes]
rs1088319	0.82[ASN][1000 genomes]
rs11164874	0.82[EUR][1000 genomes]
rs11164878	0.90[EUR][1000 genomes]
rs11164882	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11164888	0.84[EUR][1000 genomes]
rs11164889	0.84[EUR][1000 genomes]
rs11164890	0.84[EUR][1000 genomes]
rs11164891	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11164906	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11164911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11582703	0.83[EUR][1000 genomes]
rs11584466	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11799928	1.00[JPT][hapmap]
rs11800760	1.00[JPT][hapmap]
rs11801175	1.00[JPT][hapmap]
rs11801977	1.00[JPT][hapmap]
rs11802420	1.00[JPT][hapmap]
rs11807404	1.00[JPT][hapmap]
rs11808445	1.00[JPT][hapmap]
rs12057476	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs12064785	0.82[EUR][1000 genomes]
rs12066315	0.83[EUR][1000 genomes]
rs12067005	0.81[CEU][hapmap]
rs12070900	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs12071627	0.83[EUR][1000 genomes]
rs12080715	0.83[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12087466	0.82[EUR][1000 genomes]
rs12088338	0.96[EUR][1000 genomes]
rs12090723	0.83[EUR][1000 genomes]
rs12094547	0.82[EUR][1000 genomes]
rs12731675	0.83[EUR][1000 genomes]
rs12731809	0.83[EUR][1000 genomes]
rs1323628	1.00[CEU][hapmap]
rs1414367	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs1535698	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap]
rs1570528	1.00[CEU][hapmap]
rs17131699	0.81[CEU][hapmap];0.84[EUR][1000 genomes]
rs2031224	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2104280	0.82[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2749735	0.90[EUR][1000 genomes]
rs2783492	0.90[EUR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.96[EUR][1000 genomes]
rs2783506	0.90[EUR][1000 genomes]
rs2815408	0.92[EUR][1000 genomes]
rs2815409	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs2815410	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2815411	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2815412	0.92[EUR][1000 genomes]
rs2815413	1.00[CEU][hapmap];1.00[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];0.91[ASN][1000 genomes]
rs2815414	0.98[EUR][1000 genomes]
rs3171	1.00[JPT][hapmap]
rs36057148	0.81[EUR][1000 genomes]
rs41528947	1.00[JPT][hapmap]
rs4573531	0.83[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap]
rs4847407	0.84[EUR][1000 genomes]
rs4847409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs485622	0.89[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs505531	0.97[EUR][1000 genomes]
rs506556	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs508942	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs512361	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs519723	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs523262	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs546	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs556888	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs558667	0.83[EUR][1000 genomes]
rs559397	0.83[EUR][1000 genomes]
rs56303209	0.83[EUR][1000 genomes]
rs566743	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs571212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs573056	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs581825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs587754	0.83[EUR][1000 genomes]
rs605759	0.90[EUR][1000 genomes]
rs615416	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs626714	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs629153	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs631966	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs633789	0.91[CEU][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs637198	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs641390	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6541348	1.00[JPT][hapmap]
rs6541351	0.91[CEU][hapmap]
rs6541360	1.00[JPT][hapmap]
rs6541400	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs658178	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs661566	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs662546	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6657587	0.84[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap]
rs6667540	1.00[JPT][hapmap]
rs6667701	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs6671070	1.00[JPT][hapmap]
rs667680	0.95[EUR][1000 genomes]
rs6679304	1.00[JPT][hapmap]
rs6687359	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs668944	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6689867	1.00[JPT][hapmap]
rs6701250	1.00[CEU][hapmap]
rs6704067	1.00[JPT][hapmap]
rs670650	0.85[EUR][1000 genomes]
rs671559	0.96[EUR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7413775	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7518171	1.00[JPT][hapmap]
rs7519163	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7525189	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7529230	1.00[JPT][hapmap]
rs7529639	0.90[AMR][1000 genomes]
rs7532015	0.82[ASN][1000 genomes]
rs7545358	1.00[JPT][hapmap]
rs7551635	0.83[EUR][1000 genomes]
rs7554595	0.91[ASN][1000 genomes]
rs7555292	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs771449	0.90[AMR][1000 genomes]
rs771450	0.90[AMR][1000 genomes]
rs771451	0.90[AMR][1000 genomes]
rs771453	0.90[AMR][1000 genomes]
rs771457	1.00[CEU][hapmap]
rs771459	1.00[CEU][hapmap];0.90[AMR][1000 genomes]
rs771463	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap]
rs771469	1.00[CEU][hapmap]
rs771475	1.00[CEU][hapmap]
rs771477	1.00[CEU][hapmap]
rs797660	0.95[EUR][1000 genomes]
rs797669	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs809515	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs812789	1.00[CEU][hapmap]
rs8489	1.00[JPT][hapmap]
rs8561	1.00[JPT][hapmap]
rs9432680	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9432700	0.83[EUR][1000 genomes]
rs9432701	0.84[AMR][1000 genomes];0.85[EUR][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	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
2	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:15)

SNP	Gene	Cis/trans	Tissue	Source
rs522999	RP4-717I23.3	cis	lung	GTEx
rs522999	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs522999	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs522999	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs522999	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs522999	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs522999	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs522999	RP4-717I23.3	cis	Artery Aorta	GTEx
rs522999	RP4-717I23.3	cis	Stomach	GTEx
rs522999	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs522999	RP4-717I23.3	cis	Artery Tibial	GTEx
rs522999	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs522999	RP4-717I23.3	cis	Whole Blood	GTEx
rs522999	RP4-717I23.3	cis	Thyroid	GTEx
rs522999	LOC646848	cis	normal skin	skin_eQTL

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93647000-93688000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr1:93647000-93688600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:93647000-93756400	Weak transcription	Gastric	stomach
4	chr1:93647200-93681200	Weak transcription	HUVEC	blood vessel
5	chr1:93647200-93684400	Weak transcription	NH-A	brain
6	chr1:93647200-93685000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr1:93647200-93707400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:93647200-93757600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr1:93647600-93706600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr1:93649000-93684800	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr1:93651000-93684800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:93651400-93678000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:93654200-93708400	Weak transcription	Esophagus	oesophagus
14	chr1:93654600-93708000	Weak transcription	Ovary	ovary
15	chr1:93656400-93686200	Weak transcription	Aorta	Aorta
16	chr1:93657000-93682000	Strong transcription	Dnd41	blood
17	chr1:93657600-93708400	Weak transcription	Left Ventricle	heart
18	chr1:93658600-93684800	Weak transcription	Primary T cells from cord blood	blood
19	chr1:93658800-93684400	Weak transcription	Osteobl	bone
20	chr1:93660600-93705200	Weak transcription	Lung	lung
21	chr1:93660800-93685000	Weak transcription	Primary T cells fromperipheralblood	blood
22	chr1:93661400-93708200	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:93661800-93702800	Weak transcription	Fetal Heart	heart
24	chr1:93661800-93708200	Weak transcription	Fetal Brain Female	brain
25	chr1:93663600-93705600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr1:93665400-93684200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
27	chr1:93665400-93684400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr1:93665400-93685000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr1:93665400-93688800	Weak transcription	NHLF	lung
30	chr1:93665400-93708400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
31	chr1:93665400-93708400	Weak transcription	Spleen	Spleen
32	chr1:93665600-93683000	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:93665600-93697600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:93665600-93702600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:93665600-93707800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr1:93665800-93684200	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr1:93665800-93684400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:93665800-93693200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:93665800-93706600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
40	chr1:93665800-93707800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:93666200-93684200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:93666600-93727000	Weak transcription	Rectal Mucosa Donor 31	rectum
43	chr1:93666800-93675800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:93667400-93675600	Strong transcription	Fetal Thymus	thymus
45	chr1:93667400-93687600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr1:93667400-93695400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr1:93668000-93683600	Weak transcription	Adipose Nuclei	Adipose
48	chr1:93668600-93683400	Weak transcription	NHDF-Ad	bronchial
49	chr1:93668600-93684200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr1:93668800-93685200	Weak transcription	Muscle Satellite Cultured Cells	--

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