Variant report

Variant	rs771457
Chromosome Location	chr1:93827456-93827457
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93810776..93812361-chr1:93825332..93827504,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000223745	Chromatin interaction
ENSG00000117505	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:138)

rs_ID	r²[population]
rs1000606	0.90[EUR][1000 genomes]
rs10430073	0.90[EUR][1000 genomes]
rs10782958	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1081523	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1081524	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1081525	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1081526	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10874765	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10874767	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs10874771	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10874774	0.86[EUR][1000 genomes]
rs10874775	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1088319	0.82[EUR][1000 genomes]
rs11164878	0.87[AMR][1000 genomes]
rs11164882	0.86[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs11164888	0.92[EUR][1000 genomes]
rs11164889	0.92[EUR][1000 genomes]
rs11164890	0.92[EUR][1000 genomes]
rs11164891	0.88[EUR][1000 genomes]
rs11164906	0.90[EUR][1000 genomes]
rs11164911	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11582703	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11584466	0.90[EUR][1000 genomes]
rs12070900	0.85[CEU][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12071627	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12080715	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12085959	1.00[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12088338	0.84[AMR][1000 genomes]
rs12090723	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12731675	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12731809	0.93[EUR][1000 genomes]
rs1323626	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1323627	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1323628	1.00[CEU][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1414367	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes]
rs1535698	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1535700	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs1570528	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2031223	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2031224	0.90[EUR][1000 genomes]
rs2104280	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2484485	1.00[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs2783492	0.87[AMR][1000 genomes]
rs2783498	0.92[CEU][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes]
rs2783506	0.87[AMR][1000 genomes]
rs2815408	0.87[AMR][1000 genomes]
rs2815409	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes]
rs2815410	0.93[CEU][hapmap];0.91[YRI][hapmap];0.87[AMR][1000 genomes]
rs2815411	1.00[CEU][hapmap];0.90[YRI][hapmap];0.87[AMR][1000 genomes]
rs2815412	0.84[AMR][1000 genomes]
rs2815413	1.00[CEU][hapmap]
rs4573531	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4847239	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4847407	0.91[EUR][1000 genomes]
rs4847409	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs4847411	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs485622	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs488646	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs504810	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs505531	0.87[AMR][1000 genomes]
rs506556	1.00[CEU][hapmap]
rs508942	0.89[EUR][1000 genomes]
rs512361	0.90[EUR][1000 genomes]
rs519723	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs522999	1.00[CEU][hapmap]
rs523262	0.88[EUR][1000 genomes]
rs546	0.87[AMR][1000 genomes]
rs556888	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs558667	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs559397	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs56303209	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs566743	0.86[EUR][1000 genomes]
rs571212	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs573056	1.00[CEU][hapmap]
rs581825	1.00[CEU][hapmap]
rs587754	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs605759	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs626714	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs628714	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs629153	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs631966	0.90[EUR][1000 genomes]
rs633789	0.93[CEU][hapmap];0.90[EUR][1000 genomes]
rs637198	0.89[EUR][1000 genomes]
rs641390	0.89[EUR][1000 genomes]
rs6541351	0.93[CEU][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6541400	0.90[EUR][1000 genomes]
rs658178	1.00[CEU][hapmap];0.91[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs658877	1.00[CEU][hapmap]
rs661566	0.84[EUR][1000 genomes]
rs662546	0.84[EUR][1000 genomes]
rs6657587	0.92[EUR][1000 genomes]
rs6664886	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6667701	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs667680	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6687359	0.90[EUR][1000 genomes]
rs668944	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs6701250	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs670650	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs671559	0.87[AMR][1000 genomes]
rs693872	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs698926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7413775	0.90[EUR][1000 genomes]
rs7519163	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7525189	0.90[EUR][1000 genomes]
rs7529639	0.96[EUR][1000 genomes]
rs7546661	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7551635	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7555292	1.00[CEU][hapmap];0.94[YRI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs771448	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs771449	0.96[EUR][1000 genomes]
rs771450	0.96[EUR][1000 genomes]
rs771451	0.96[EUR][1000 genomes]
rs771452	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771453	0.96[EUR][1000 genomes]
rs771455	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs771456	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs771459	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs771460	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs771463	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs771464	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771466	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771467	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771468	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771469	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771471	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs771475	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771477	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs771480	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs797660	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs797669	0.83[EUR][1000 genomes]
rs809515	0.83[EUR][1000 genomes]
rs810028	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs812789	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9432680	0.89[EUR][1000 genomes]
rs9432700	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9432701	0.89[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs771457	RP4-717I23.3	cis	Artery Aorta	GTEx
rs771457	RP4-717I23.3	cis	Adipose Subcutaneous	GTEx
rs771457	RP4-717I23.3	cis	Heart Left Ventricle	GTEx
rs771457	RP4-717I23.3	cis	Nerve Tibial	GTEx
rs771457	RP4-717I23.3	cis	Esophagus Muscularis	GTEx
rs771457	RP4-717I23.3	cis	Stomach	GTEx
rs771457	RP4-717I23.3	cis	Thyroid	GTEx
rs771457	RP4-717I23.3	cis	lung	GTEx
rs771457	RP4-717I23.3	cis	Esophagus Mucosa	GTEx
rs771457	RP4-717I23.3	cis	Artery Tibial	GTEx
rs771457	LOC646848	cis	normal skin	skin_eQTL
rs771457	RP4-717I23.3	cis	Skin Sun Exposed Lower leg	GTEx
rs771457	RP4-717I23.3	cis	Whole Blood	GTEx
rs771457	RP4-717I23.3	cis	Muscle Skeletal	GTEx
rs771457	TMED5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93812800-93831000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:93812800-93832200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr1:93813400-93840000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:93813400-93840400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:93815400-93839800	Weak transcription	Aorta	Aorta
6	chr1:93815600-93834800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:93816000-93832200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:93816600-93841800	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:93816800-93841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr1:93817800-93832400	Weak transcription	Psoas Muscle	Psoas
11	chr1:93818000-93835400	Weak transcription	Small Intestine	intestine
12	chr1:93818400-93836000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr1:93818800-93837200	Weak transcription	Fetal Kidney	kidney
14	chr1:93819000-93828000	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr1:93819000-93833200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr1:93819400-93832000	Strong transcription	HSMM	muscle
17	chr1:93819400-93834600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr1:93819600-93830000	Strong transcription	HMEC	breast
19	chr1:93819800-93827600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:93819800-93829800	Strong transcription	NHDF-Ad	bronchial
21	chr1:93819800-93830800	Weak transcription	Rectal Smooth Muscle	rectum
22	chr1:93820200-93828200	Strong transcription	Primary hematopoietic stem cells	blood
23	chr1:93820600-93837200	Weak transcription	Colonic Mucosa	Colon
24	chr1:93821000-93838800	Weak transcription	Ovary	ovary
25	chr1:93821200-93835200	Weak transcription	Stomach Smooth Muscle	stomach
26	chr1:93822200-93835800	Strong transcription	Dnd41	blood
27	chr1:93822200-93840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr1:93823800-93827600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:93823800-93834600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:93824000-93830000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:93824000-93831000	Weak transcription	Fetal Brain Male	brain
32	chr1:93824200-93828600	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr1:93824200-93828600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:93824200-93829400	Weak transcription	NHLF	lung
35	chr1:93824200-93830600	Weak transcription	Fetal Muscle Trunk	muscle
36	chr1:93824200-93830800	Weak transcription	Left Ventricle	heart
37	chr1:93824200-93832000	Weak transcription	Fetal Stomach	stomach
38	chr1:93824200-93832200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:93824200-93832200	Weak transcription	Fetal Intestine Small	intestine
40	chr1:93824200-93833000	Weak transcription	Esophagus	oesophagus
41	chr1:93824200-93833000	Weak transcription	Gastric	stomach
42	chr1:93824200-93833400	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr1:93824200-93838200	Weak transcription	Pancreas	Pancrea
44	chr1:93824200-93839400	Weak transcription	Lung	lung
45	chr1:93824200-93839800	Weak transcription	Fetal Brain Female	brain
46	chr1:93824200-93840000	Weak transcription	Right Ventricle	heart
47	chr1:93824200-93841000	Weak transcription	Brain Germinal Matrix	brain
48	chr1:93824200-93841000	Weak transcription	Spleen	Spleen
49	chr1:93824400-93829000	Weak transcription	Fetal Lung	lung
50	chr1:93824400-93831200	Weak transcription	H1 Cell Line	embryonic stem cell

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