Variant report

Variant	rs13240501
Chromosome Location	chr7:66038472-66038473
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	chr7:66030313..66032213-chr7:66037914..66039587,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 20 )

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

rs_ID	r²[population]
rs10107	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10265311	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10271548	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10274883	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10278014	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10807704	0.80[AFR][1000 genomes]
rs10950043	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10950046	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10950050	0.84[EUR][1000 genomes]
rs11761542	0.87[EUR][1000 genomes]
rs11763189	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11765791	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11772819	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11772884	0.99[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11773628	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12333370	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12668005	0.80[AFR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12673450	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12698522	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12698526	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13226170	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13226966	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs13232191	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13242290	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13308803	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13536	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1544549	0.81[AFR][1000 genomes]
rs1623000	0.80[ASN][1000 genomes]
rs17747530	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1860469	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1860472	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1968126	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2013908	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2024192	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2109295	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2109297	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2420608	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2420610	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2420611	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2420820	0.81[AFR][1000 genomes]
rs2420821	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2659890	0.88[EUR][1000 genomes]
rs2659891	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2659892	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2659893	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2659896	0.87[EUR][1000 genomes]
rs2659898	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2659901	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2659907	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2659908	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2707824	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2707837	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2707847	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs28431318	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28480509	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28617601	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs28714531	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28731376	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2901209	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs35378740	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3846973	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3857685	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3926380	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4506088	0.82[AFR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4717315	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718377	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718383	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57739047	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs58347342	0.87[EUR][1000 genomes]
rs61348003	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6460301	0.85[AFR][1000 genomes]
rs6460302	0.85[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs6460303	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460304	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs66981195	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6945775	0.85[AFR][1000 genomes]
rs6951302	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6951946	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6955837	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6958200	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6971059	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6973249	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6975044	0.83[EUR][1000 genomes]
rs6978028	0.80[AFR][1000 genomes]
rs6978178	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6980451	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs721717	0.88[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7384021	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7385102	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7778322	0.80[AFR][1000 genomes]
rs7782587	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs778697	0.80[AFR][1000 genomes]
rs7789615	0.80[AFR][1000 genomes]
rs7792762	0.83[AFR][1000 genomes]
rs7793723	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7800620	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7805152	0.86[EUR][1000 genomes]
rs7808013	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801194	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs801195	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801202	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801203	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801204	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801206	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs801208	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801209	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs801215	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs881285	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9791712	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9791713	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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	nsv888326	chr7:65825257-66066999	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
6	nsv482441	chr7:65885824-66061788	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv3377926	chr7:65934493-66051484	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
8	esv3423847	chr7:65941210-66054107	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
9	nsv970868	chr7:66035219-66056610	Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs13240501	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs13240501	GS1-124K5.11	cis	Thyroid	GTEx
rs13240501	GS1-124K5.2	cis	Whole Blood	GTEx
rs13240501	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs13240501	RP4-756H11.3	cis	Thyroid	GTEx
rs13240501	GTF2IRD1P1	cis	Thyroid	GTEx
rs13240501	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13240501	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs13240501	LINC00174	cis	Thyroid	GTEx
rs13240501	GS1-124K5.4	cis	Stomach	GTEx
rs13240501	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs13240501	RP4-756H11.3	cis	lung	GTEx
rs13240501	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13240501	RNU6-96P	cis	Thyroid	GTEx
rs13240501	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs13240501	GS1-124K5.4	cis	Artery Aorta	GTEx
rs13240501	RP4-756H11.3	cis	Artery Tibial	GTEx
rs13240501	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs13240501	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs13240501	RP4-756H11.3	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66004400-66052600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:66008600-66056000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr7:66011600-66045000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr7:66021800-66056400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr7:66022000-66039000	Weak transcription	Aorta	Aorta
6	chr7:66023000-66040800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr7:66023000-66041800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr7:66023200-66043800	Weak transcription	Fetal Heart	heart
9	chr7:66023200-66044400	Weak transcription	Right Atrium	heart
10	chr7:66023200-66048400	Weak transcription	Colon Smooth Muscle	Colon
11	chr7:66023200-66049800	Weak transcription	Stomach Mucosa	stomach
12	chr7:66023200-66055400	Weak transcription	Fetal Brain Male	brain
13	chr7:66023600-66042200	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr7:66024000-66039000	Weak transcription	Right Ventricle	heart
15	chr7:66024000-66046400	Weak transcription	NHLF	lung
16	chr7:66024200-66040400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr7:66024200-66051200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr7:66024200-66055400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr7:66024200-66055600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr7:66024400-66038800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr7:66024400-66051600	Weak transcription	Spleen	Spleen
22	chr7:66027600-66042400	Strong transcription	Primary monocytes fromperipheralblood	blood
23	chr7:66028600-66038800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr7:66028600-66042000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr7:66028800-66042000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:66028800-66042000	Strong transcription	Primary B cells from peripheral blood	blood
27	chr7:66029000-66041400	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr7:66029000-66042000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr7:66029000-66042800	Strong transcription	Dnd41	blood
30	chr7:66029200-66038800	Strong transcription	K562	blood
31	chr7:66029400-66038800	Weak transcription	Gastric	stomach
32	chr7:66029400-66038800	Weak transcription	Ovary	ovary
33	chr7:66029400-66046200	Weak transcription	Pancreas	Pancrea
34	chr7:66030000-66038800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr7:66030400-66039400	Strong transcription	Liver	Liver
36	chr7:66030400-66040400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr7:66030600-66042600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr7:66031000-66041800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr7:66031200-66039400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr7:66031200-66040000	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr7:66031400-66042000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr7:66031600-66045200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr7:66032000-66038800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr7:66032200-66040000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr7:66032400-66041600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr7:66032600-66041600	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr7:66032800-66039800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr7:66033000-66043400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr7:66033200-66042000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr7:66033600-66042000	Strong transcription	Fetal Intestine Large	intestine

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