Variant report

Variant	rs11164878
Chromosome Location	chr1:93639823-93639824
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93638069..93640973-chr1:93641703..93643320,2	K562	blood:
2	chr1:93632484..93634850-chr1:93639187..93641341,2	K562	blood:
3	chr1:93635790..93638492-chr1:93639188..93641506,2	K562	blood:

Extended variants
information (count: 111 )
Associated
traits (count: 14 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1000606	0.80[EUR][1000 genomes]
rs10430073	0.80[EUR][1000 genomes]
rs10782958	0.82[EUR][1000 genomes]
rs1081526	0.87[AMR][1000 genomes]
rs10874765	0.82[EUR][1000 genomes]
rs10874767	0.82[EUR][1000 genomes]
rs10874771	0.82[EUR][1000 genomes]
rs11164874	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11164882	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11164888	0.82[EUR][1000 genomes]
rs11164889	0.82[EUR][1000 genomes]
rs11164890	0.82[EUR][1000 genomes]
rs11164906	0.80[EUR][1000 genomes]
rs11582703	0.82[EUR][1000 genomes]
rs11584466	0.80[EUR][1000 genomes]
rs11586323	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12057476	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12064785	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12066315	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12067005	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12070900	0.82[EUR][1000 genomes]
rs12071627	0.82[EUR][1000 genomes]
rs12080715	0.82[EUR][1000 genomes]
rs12085959	0.82[EUR][1000 genomes]
rs12087466	0.87[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs12088338	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12090723	0.82[EUR][1000 genomes]
rs12094547	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12731675	0.82[EUR][1000 genomes]
rs12731809	0.82[EUR][1000 genomes]
rs1323626	0.87[AMR][1000 genomes]
rs1323628	0.84[AMR][1000 genomes]
rs1414367	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1535698	0.82[EUR][1000 genomes]
rs17131699	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2031224	0.80[EUR][1000 genomes]
rs2104280	0.81[EUR][1000 genomes]
rs2391227	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2484485	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2749735	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2783492	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2783498	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2783506	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2815408	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815409	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815410	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815411	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815412	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815413	0.90[EUR][1000 genomes]
rs2815414	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs36057148	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4573531	0.82[EUR][1000 genomes]
rs4847407	0.81[EUR][1000 genomes]
rs4847409	0.80[EUR][1000 genomes]
rs485622	0.83[EUR][1000 genomes]
rs504810	0.81[EUR][1000 genomes]
rs505531	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs506556	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs512361	0.80[EUR][1000 genomes]
rs519723	0.82[EUR][1000 genomes]
rs522999	0.90[EUR][1000 genomes]
rs546	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs556888	0.80[EUR][1000 genomes]
rs55701931	0.89[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs558667	0.82[EUR][1000 genomes]
rs559397	0.82[EUR][1000 genomes]
rs56303209	0.82[EUR][1000 genomes]
rs571212	0.83[EUR][1000 genomes]
rs573056	0.88[EUR][1000 genomes]
rs581825	0.89[EUR][1000 genomes]
rs587754	0.82[EUR][1000 genomes]
rs605759	0.84[EUR][1000 genomes]
rs615416	0.90[EUR][1000 genomes]
rs626714	0.82[EUR][1000 genomes]
rs629153	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs631966	0.80[EUR][1000 genomes]
rs633789	0.80[EUR][1000 genomes]
rs6541400	0.80[EUR][1000 genomes]
rs658178	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs658877	0.90[EUR][1000 genomes]
rs661566	0.81[EUR][1000 genomes]
rs662546	0.81[EUR][1000 genomes]
rs6657587	0.82[EUR][1000 genomes]
rs6667701	0.82[EUR][1000 genomes]
rs667680	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6687359	0.80[EUR][1000 genomes]
rs670650	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs671559	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs693872	0.80[EUR][1000 genomes]
rs698926	0.87[AMR][1000 genomes]
rs71510760	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs7413775	0.80[EUR][1000 genomes]
rs7519163	0.80[EUR][1000 genomes]
rs7525189	0.80[EUR][1000 genomes]
rs7551635	0.82[EUR][1000 genomes]
rs7555292	0.82[EUR][1000 genomes]
rs771452	0.87[AMR][1000 genomes]
rs771457	0.87[AMR][1000 genomes]
rs771460	0.87[AMR][1000 genomes]
rs771464	0.81[AMR][1000 genomes]
rs771466	0.87[AMR][1000 genomes]
rs771472	0.87[AMR][1000 genomes]
rs771474	0.87[AMR][1000 genomes]
rs771480	0.87[AMR][1000 genomes]
rs797660	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs797669	0.80[EUR][1000 genomes]
rs809515	0.83[EUR][1000 genomes]
rs9432700	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:14)

SNP	Gene	Cis/trans	Tissue	Source
rs11164878	RP4-717I23.3	cis	Artery Tibial	GTEx
rs11164878	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs11164878	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs11164878	RP4-717I23.3	cis	Whole Blood	GTEx
rs11164878	RP4-717I23.3	cis	lung	GTEx
rs11164878	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs11164878	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs11164878	RP4-717I23.3	cis	Thyroid	GTEx
rs11164878	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs11164878	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs11164878	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs11164878	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs11164878	RP4-717I23.3	cis	Artery Aorta	GTEx
rs11164878	RP4-717I23.3	cis	Stomach	GTEx

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:93582400-93642800	Weak transcription	Gastric	stomach
3	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
4	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
5	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:93615600-93643200	Weak transcription	Fetal Kidney	kidney
8	chr1:93621400-93640000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:93621400-93643000	Weak transcription	HMEC	breast
10	chr1:93621400-93643800	Weak transcription	Colonic Mucosa	Colon
11	chr1:93621600-93641400	Weak transcription	NHEK	skin
12	chr1:93624000-93643400	Weak transcription	NH-A	brain
13	chr1:93624000-93643600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:93624400-93643600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr1:93624800-93641600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr1:93624800-93643600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr1:93624800-93643600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr1:93625000-93640000	Weak transcription	K562	blood
19	chr1:93625000-93641200	Weak transcription	HSMM	muscle
20	chr1:93625800-93640200	Weak transcription	HUVEC	blood vessel
21	chr1:93625800-93641600	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr1:93625800-93643400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr1:93626000-93641200	Weak transcription	NHDF-Ad	bronchial
24	chr1:93630400-93641600	Weak transcription	Right Atrium	heart
25	chr1:93630800-93642000	Weak transcription	Left Ventricle	heart
26	chr1:93632800-93640000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:93633400-93643600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr1:93634200-93642000	Weak transcription	Brain Anterior Caudate	brain
29	chr1:93634400-93640200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:93634600-93643000	Weak transcription	Right Ventricle	heart
31	chr1:93636200-93640000	Weak transcription	Thymus	Thymus
32	chr1:93636200-93642200	Weak transcription	Lung	lung
33	chr1:93636200-93642800	Weak transcription	Fetal Brain Female	brain
34	chr1:93636200-93642800	Weak transcription	Pancreas	Pancrea
35	chr1:93636200-93643200	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr1:93636200-93643400	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr1:93636200-93644000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:93636200-93644800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:93636400-93640200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:93636400-93642000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr1:93636400-93643800	Weak transcription	Fetal Stomach	stomach
42	chr1:93636600-93641600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:93636600-93641600	Weak transcription	Spleen	Spleen
44	chr1:93636600-93642000	Weak transcription	Fetal Intestine Small	intestine
45	chr1:93636600-93642200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr1:93636600-93642800	Weak transcription	Fetal Muscle Leg	muscle
47	chr1:93637000-93640000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr1:93637000-93640000	Weak transcription	Fetal Thymus	thymus
49	chr1:93637000-93640000	Enhancers	HepG2	liver
50	chr1:93637200-93640000	Enhancers	Primary T helper cells fromperipheralblood	blood

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