Variant report

Variant	rs546
Chromosome Location	chr1:93617546-93617547
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:93615373..93618424-chr1:93643538..93645744,3	K562	blood:
2	chr1:93610795..93612747-chr1:93615451..93618016,2	K562	blood:
3	chr1:93606473..93608492-chr1:93616933..93619902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000122483	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10782958	0.81[EUR][1000 genomes]
rs1081526	0.87[AMR][1000 genomes]
rs10874765	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs10874771	0.81[EUR][1000 genomes]
rs11164874	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11164878	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11164882	0.85[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11164911	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs11582703	0.81[EUR][1000 genomes]
rs11586323	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12057476	1.00[ASW][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12064785	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12066315	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12067005	0.91[ASW][hapmap];0.92[LWK][hapmap];0.88[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs12070900	0.84[CEU][hapmap];0.94[YRI][hapmap];0.81[EUR][1000 genomes]
rs12071627	0.81[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs12087466	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs12088338	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12090723	0.81[EUR][1000 genomes]
rs12094547	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12731675	0.81[EUR][1000 genomes]
rs12731809	0.81[EUR][1000 genomes]
rs1323626	0.87[AMR][1000 genomes]
rs1323628	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes]
rs1414367	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1535698	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap]
rs17131699	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]
rs2391227	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2749735	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2783492	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2783506	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2815408	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2815410	0.93[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815411	1.00[CEU][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2815412	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2815413	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2815414	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36057148	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4573531	0.81[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs4847409	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs485622	0.82[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap]
rs504810	1.00[CEU][hapmap]
rs505531	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs506556	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs519723	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.81[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs556888	1.00[CEU][hapmap]
rs55701931	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs559397	0.81[EUR][1000 genomes]
rs56303209	0.81[EUR][1000 genomes]
rs571212	1.00[CEU][hapmap];0.83[GIH][hapmap];0.92[TSI][hapmap];0.81[EUR][1000 genomes]
rs573056	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap];0.86[EUR][1000 genomes]
rs581825	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs587754	0.81[EUR][1000 genomes]
rs605759	0.83[EUR][1000 genomes]
rs615416	0.89[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs628714	1.00[CEU][hapmap]
rs629153	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs633789	0.93[CEU][hapmap];0.92[TSI][hapmap]
rs6541351	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs658178	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs658877	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.93[YRI][hapmap]
rs6667701	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs667680	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs668944	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs6701250	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap]
rs670650	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs671559	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs693872	1.00[CEU][hapmap]
rs698926	0.87[AMR][1000 genomes]
rs71510760	0.87[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7519163	1.00[CEU][hapmap];0.83[GIH][hapmap];0.96[TSI][hapmap]
rs7551635	0.81[EUR][1000 genomes]
rs7555292	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs771452	0.87[AMR][1000 genomes]
rs771457	0.87[AMR][1000 genomes]
rs771460	0.87[AMR][1000 genomes]
rs771463	1.00[CEU][hapmap];0.96[TSI][hapmap]
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	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs809515	0.81[EUR][1000 genomes]
rs9432700	0.81[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:17)

SNP	Gene	Cis/trans	Tissue	Source
rs546	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs546	RP4-717I23.3	cis	Stomach	GTEx
rs546	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs546	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs546	LOC646848	cis	normal skin	skin_eQTL
rs546	RP4-717I23.3	cis	lung	GTEx
rs546	RP4-717I23.3	cis	Artery Tibial	GTEx
rs546	TMED5	Cis_1M	lymphoblastoid	RTeQTL
rs546	TMED5	cis	cerebellum	SCAN
rs546	RP4-717I23.3	cis	Thyroid	GTEx
rs546	RP4-717I23.3	cis	Artery Aorta	GTEx
rs546	RP4-717I23.3	cis	Whole Blood	GTEx
rs546	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs546	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs546	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs546	TMED5	cis	parietal	SCAN
rs546	RP4-717I23.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93565200-93625200	Weak transcription	Stomach Mucosa	stomach
2	chr1:93573400-93627000	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:93574600-93630200	Weak transcription	Right Ventricle	heart
4	chr1:93578800-93620600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:93580000-93624000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr1:93580200-93643600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:93582400-93620400	Weak transcription	Small Intestine	intestine
8	chr1:93582400-93642800	Weak transcription	Gastric	stomach
9	chr1:93583200-93628800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:93583600-93623800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:93583600-93635400	Weak transcription	Pancreas	Pancrea
12	chr1:93585800-93642200	Weak transcription	Esophagus	oesophagus
13	chr1:93586200-93623400	Weak transcription	Fetal Brain Male	brain
14	chr1:93586800-93621000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr1:93595800-93635600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:93597400-93625400	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:93600400-93635400	Weak transcription	Spleen	Spleen
18	chr1:93601000-93643600	Weak transcription	HSMMtube	muscle
19	chr1:93601400-93635400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr1:93602600-93620400	Weak transcription	Fetal Stomach	stomach
21	chr1:93602600-93620600	Weak transcription	Colonic Mucosa	Colon
22	chr1:93602600-93620600	Weak transcription	Fetal Intestine Small	intestine
23	chr1:93602600-93624200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr1:93602600-93628800	Weak transcription	Aorta	Aorta
25	chr1:93602600-93630200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:93602600-93630200	Weak transcription	Brain Anterior Caudate	brain
27	chr1:93603400-93620800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr1:93603400-93624600	Weak transcription	Brain Substantia Nigra	brain
29	chr1:93603600-93620000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:93603600-93620600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr1:93603600-93621800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr1:93603600-93629200	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr1:93603800-93620000	Weak transcription	Fetal Lung	lung
34	chr1:93604400-93618400	Weak transcription	HepG2	liver
35	chr1:93604600-93620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr1:93606000-93644600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:93606800-93621800	Weak transcription	Brain Germinal Matrix	brain
38	chr1:93606800-93623600	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr1:93606800-93635400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr1:93608800-93617800	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr1:93609000-93627400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:93611200-93626200	Strong transcription	Fetal Thymus	thymus
43	chr1:93611800-93644600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:93612600-93620200	Strong transcription	Dnd41	blood
45	chr1:93612800-93619600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr1:93613000-93626000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:93613000-93626000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr1:93613200-93625000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr1:93613200-93626200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:93613200-93627800	Strong transcription	Primary monocytes fromperipheralblood	blood

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