Variant report

Variant	rs28480509
Chromosome Location	chr7:66099224-66099225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:66093935..66096906-chr7:66098680..66103505,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 20 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10107	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10233806	0.88[AFR][1000 genomes]
rs10244498	0.88[AFR][1000 genomes]
rs10265311	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10271548	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10274883	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10278014	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950043	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950046	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10950049	0.83[AFR][1000 genomes]
rs10950050	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11761542	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11763189	0.82[EUR][1000 genomes]
rs11765791	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772819	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11772884	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11773628	0.82[EUR][1000 genomes]
rs12333370	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12668005	0.86[ASN][1000 genomes]
rs12673450	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698522	0.81[EUR][1000 genomes]
rs12698526	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13226170	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13226966	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13232191	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13240501	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13242290	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13308803	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13536	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1544549	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs1623000	0.86[ASN][1000 genomes]
rs17747530	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1860469	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860472	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968126	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2003300	0.84[AFR][1000 genomes]
rs2013908	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2024192	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2109295	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109297	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2420610	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2420611	0.82[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2420820	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2420821	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2659890	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2659891	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659892	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659893	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659894	0.84[AFR][1000 genomes]
rs2659895	0.84[AFR][1000 genomes]
rs2659896	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2659897	0.84[AFR][1000 genomes]
rs2659898	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659900	0.86[AFR][1000 genomes]
rs2659901	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659904	0.86[AFR][1000 genomes]
rs2659907	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2659908	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2707824	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2707837	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2707839	0.84[AFR][1000 genomes]
rs2707847	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28431318	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28617601	0.81[EUR][1000 genomes]
rs28714531	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28731376	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2901209	0.82[EUR][1000 genomes]
rs35378740	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846973	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3857685	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3926380	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4506088	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4610622	0.83[AFR][1000 genomes]
rs4717315	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4718377	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718383	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58347342	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61348003	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460303	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66981195	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6951302	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6951946	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955837	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958200	0.84[AFR][1000 genomes]
rs6969679	0.82[AFR][1000 genomes]
rs6971059	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6973249	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6975044	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6978178	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs721717	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7384021	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7385102	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7782587	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7793723	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7800620	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7805152	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7808013	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801194	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801195	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801202	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801203	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801204	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801206	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801208	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801209	0.80[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801215	0.86[ASN][1000 genomes]
rs881285	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs974239	0.84[AFR][1000 genomes]
rs9791712	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791713	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv1035107	chr7:65814901-66114919	Genic enhancers Strong transcription ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
4	nsv538909	chr7:65814901-66114919	Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
5	esv2761151	chr7:66095738-66138285	Flanking Active TSS Strong transcription Genic enhancers Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs28480509	RP4-756H11.3	cis	Artery Tibial	GTEx
rs28480509	GS1-124K5.2	cis	Whole Blood	GTEx
rs28480509	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs28480509	GS1-124K5.4	cis	Artery Aorta	GTEx
rs28480509	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs28480509	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs28480509	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs28480509	RNU6-96P	cis	Thyroid	GTEx
rs28480509	GTF2IRD1P1	cis	Thyroid	GTEx
rs28480509	LINC00174	cis	Thyroid	GTEx
rs28480509	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs28480509	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs28480509	RP4-756H11.3	cis	Thyroid	GTEx
rs28480509	RP4-756H11.3	cis	lung	GTEx
rs28480509	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs28480509	GS1-124K5.11	cis	Thyroid	GTEx
rs28480509	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs28480509	GS1-124K5.4	cis	Stomach	GTEx
rs28480509	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs28480509	ASL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66094400-66103200	Weak transcription	Small Intestine	intestine
2	chr7:66094800-66103400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:66095000-66099400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr7:66095000-66099400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr7:66095000-66099400	Weak transcription	Aorta	Aorta
6	chr7:66095000-66099600	Weak transcription	A549	lung
7	chr7:66095000-66101000	Weak transcription	NHEK	skin
8	chr7:66095000-66102400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr7:66095000-66103000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr7:66095000-66103000	Weak transcription	Fetal Kidney	kidney
11	chr7:66095000-66103000	Weak transcription	Fetal Lung	lung
12	chr7:66095000-66103200	Weak transcription	Psoas Muscle	Psoas
13	chr7:66095000-66103400	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr7:66095000-66103400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr7:66095000-66103400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr7:66095000-66104200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr7:66095000-66108800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr7:66095000-66109000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr7:66095000-66115200	Weak transcription	HMEC	breast
20	chr7:66095200-66099400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr7:66095200-66099400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr7:66095200-66099800	Weak transcription	Colonic Mucosa	Colon
23	chr7:66095200-66101000	Weak transcription	NHDF-Ad	bronchial
24	chr7:66095200-66103000	Weak transcription	Stomach Mucosa	stomach
25	chr7:66095200-66103200	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr7:66095200-66118400	Weak transcription	Fetal Heart	heart
27	chr7:66095200-66118400	Weak transcription	HUVEC	blood vessel
28	chr7:66095400-66099400	Weak transcription	Colon Smooth Muscle	Colon
29	chr7:66095400-66101000	Weak transcription	NH-A	brain
30	chr7:66095400-66103200	Weak transcription	Pancreas	Pancrea
31	chr7:66095800-66100800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:66095800-66101000	Weak transcription	HSMM	muscle
33	chr7:66095800-66101000	Weak transcription	K562	blood
34	chr7:66095800-66102800	Weak transcription	Fetal Brain Male	brain
35	chr7:66095800-66103200	Weak transcription	Esophagus	oesophagus
36	chr7:66096000-66099400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr7:66096000-66113800	Strong transcription	Fetal Stomach	stomach
38	chr7:66096200-66101000	Weak transcription	NHLF	lung
39	chr7:66097000-66099400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr7:66097000-66113400	Strong transcription	Fetal Brain Female	brain
41	chr7:66097600-66103000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr7:66097600-66103000	Weak transcription	Dnd41	blood
43	chr7:66097800-66099400	Weak transcription	Duodenum Mucosa	Duodenum
44	chr7:66097800-66118200	Weak transcription	Primary hematopoietic stem cells	blood
45	chr7:66098000-66099800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr7:66098000-66100000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr7:66098000-66100200	Strong transcription	Cortex derived primary cultured neurospheres	brain
48	chr7:66098000-66100200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr7:66098000-66101200	Strong transcription	Brain Germinal Matrix	brain
50	chr7:66098000-66102600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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