Variant report

Variant	rs13242290
Chromosome Location	chr7:66121885-66121886
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:66116638..66119241-chr7:66120094..66122874,2	K562	blood:
2	chr7:66052648..66055044-chr7:66119940..66122450,2	K562	blood:
3	chr7:66120659..66123648-chr7:66152144..66153650,2	K562	blood:
4	chr7:66121223..66123141-chr7:66144196..66146928,3	MCF-7	breast:
5	chr7:66091844..66094640-chr7:66118336..66122170,5	MCF-7	breast:
6	chr7:66091898..66097382-chr7:66117985..66122507,10	K562	blood:

Variant related genes	Relation type
ENSG00000243335	Chromatin interaction

Extended variants
information (count: 118 )
Associated
traits (count: 20 )

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

rs_ID	r²[population]
rs10107	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10233806	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs10244498	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10265311	0.83[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10271548	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10274883	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10278014	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10950043	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950046	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10950050	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11761542	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11763189	0.81[EUR][1000 genomes]
rs11765791	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11772819	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11772884	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11773628	0.81[EUR][1000 genomes]
rs12333370	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12668005	0.86[ASN][1000 genomes]
rs12673450	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12698522	0.82[EUR][1000 genomes]
rs12698526	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13226170	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13226966	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13232191	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13240501	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13308803	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13536	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1544549	0.87[AFR][1000 genomes]
rs1623000	0.88[ASN][1000 genomes]
rs17747530	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1860469	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1860472	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1968126	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2003300	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs2013908	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2024192	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2109295	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2109297	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420610	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2420611	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2420820	0.87[AFR][1000 genomes]
rs2420821	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2659890	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2659891	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659892	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659893	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2659894	0.85[AFR][1000 genomes]
rs2659895	0.85[AFR][1000 genomes]
rs2659896	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2659897	0.85[AFR][1000 genomes]
rs2659898	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2659900	0.83[AFR][1000 genomes]
rs2659901	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2659904	0.83[AFR][1000 genomes]
rs2659907	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659908	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2659914	0.83[AMR][1000 genomes]
rs2707824	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2707837	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2707839	0.85[AFR][1000 genomes]
rs2707847	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28431318	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28480509	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28714531	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28731376	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2901209	0.81[EUR][1000 genomes]
rs35378740	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3846973	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3857685	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3926380	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4506088	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4717315	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4718377	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4718383	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58347342	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61348003	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6460302	0.80[EUR][1000 genomes]
rs6460303	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66981195	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6951302	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951946	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6955837	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6958200	0.80[AFR][1000 genomes]
rs6971059	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6973249	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6975044	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6978178	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs721717	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7384021	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7385102	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7782587	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7793723	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7800620	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7805152	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7808013	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs801194	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs801195	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801202	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801203	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801204	0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801206	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs801208	0.80[AFR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801209	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs801215	0.86[ASN][1000 genomes]
rs881285	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs974239	0.81[AFR][1000 genomes]
rs9791712	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9791713	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	esv3496297	chr7:66099491-66136579	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	esv3496298	chr7:66099491-66136579	Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
6	esv3486481	chr7:66101377-66137773	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	esv3486482	chr7:66101377-66137773	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	esv3509629	chr7:66101713-66137585	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	esv3509631	chr7:66101713-66137585	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv967445	chr7:66112743-66133589	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:20)

SNP	Gene	Cis/trans	Tissue	Source
rs13242290	RP4-756H11.3	cis	Artery Aorta	GTEx
rs13242290	GS1-124K5.2	cis	Whole Blood	GTEx
rs13242290	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs13242290	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs13242290	GS1-124K5.4	cis	Artery Aorta	GTEx
rs13242290	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13242290	RNU6-96P	cis	Thyroid	GTEx
rs13242290	GTF2IRD1P1	cis	Thyroid	GTEx
rs13242290	GS1-124K5.4	cis	Stomach	GTEx
rs13242290	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs13242290	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13242290	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs13242290	RP4-756H11.3	cis	Artery Tibial	GTEx
rs13242290	GS1-124K5.11	cis	Thyroid	GTEx
rs13242290	RP4-756H11.3	cis	lung	GTEx
rs13242290	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs13242290	RP4-756H11.3	cis	Thyroid	GTEx
rs13242290	LINC00174	cis	Thyroid	GTEx
rs13242290	RP4-756H11.3	cis	Esophagus Mucosa	GTEx
rs13242290	RP4-756H11.3	cis	Nerve Tibial	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:66120400-66127400	Weak transcription	Lung	lung
2	chr7:66120400-66127600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:66120600-66127600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:66120600-66127600	Weak transcription	Fetal Brain Male	brain
5	chr7:66120600-66127600	Weak transcription	Fetal Kidney	kidney
6	chr7:66120600-66127600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr7:66120600-66127600	Weak transcription	Thymus	Thymus
8	chr7:66120600-66129600	Weak transcription	Brain Substantia Nigra	brain
9	chr7:66120600-66129800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr7:66120600-66132400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr7:66120600-66146000	Weak transcription	Primary T cells from cord blood	blood
12	chr7:66120600-66146200	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr7:66120800-66123200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr7:66120800-66127400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr7:66120800-66127400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr7:66120800-66127600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr7:66120800-66127600	Weak transcription	Brain Germinal Matrix	brain
18	chr7:66120800-66132000	Weak transcription	Fetal Brain Female	brain
19	chr7:66120800-66143600	Weak transcription	GM12878-XiMat	blood
20	chr7:66120800-66146000	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr7:66121000-66122200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr7:66121000-66122200	Enhancers	Brain Cingulate Gyrus	brain
23	chr7:66121000-66123800	Weak transcription	Fetal Intestine Small	intestine
24	chr7:66121000-66127200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr7:66121000-66127400	Weak transcription	A549	lung
26	chr7:66121000-66127600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr7:66121000-66139400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr7:66121000-66143600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr7:66121000-66144000	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr7:66121000-66146200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr7:66121000-66146200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr7:66121200-66122200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr7:66121200-66123000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr7:66121200-66124400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr7:66121200-66127400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr7:66121200-66127400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr7:66121200-66127400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr7:66121200-66130600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr7:66121200-66131400	Weak transcription	Brain Angular Gyrus	brain
40	chr7:66121200-66137800	Weak transcription	HMEC	breast
41	chr7:66121400-66122000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr7:66121400-66122200	Enhancers	NHDF-Ad	bronchial
43	chr7:66121400-66123400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr7:66121400-66127400	Weak transcription	Fetal Lung	lung
45	chr7:66121400-66127400	Weak transcription	Spleen	Spleen
46	chr7:66121400-66127600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr7:66121400-66127600	Weak transcription	Left Ventricle	heart
48	chr7:66121400-66127600	Weak transcription	Pancreas	Pancrea
49	chr7:66121400-66130200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr7:66121400-66139800	Weak transcription	Rectal Smooth Muscle	rectum

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