Variant report

Variant	rs1909508
Chromosome Location	chr7:65766353-65766354
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65765329..65768039-chr7:65770464..65772414,2	K562	blood:
2	chr7:65759129..65761337-chr7:65764429..65766809,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs10261710	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10447522	0.82[YRI][hapmap]
rs1065265	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10950026	1.00[CEU][hapmap]
rs10950027	0.81[EUR][1000 genomes]
rs10950029	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs10950035	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10950036	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10950040	0.89[EUR][1000 genomes]
rs11763224	0.85[EUR][1000 genomes]
rs11766183	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11767262	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11769702	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11770063	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12667200	0.92[ASN][1000 genomes]
rs12668269	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12670811	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12671152	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12671834	0.82[EUR][1000 genomes]
rs12672427	0.89[EUR][1000 genomes]
rs1547529	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs160641	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs1695820	0.82[YRI][hapmap]
rs17138149	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17138156	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1862085	0.86[EUR][1000 genomes]
rs2088655	0.82[YRI][hapmap]
rs2173571	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279757	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2420456	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs313818	0.93[YRI][hapmap]
rs316305	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs316306	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs316323	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs316324	0.86[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap]
rs316328	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[GIH][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs35459055	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3735147	0.89[EUR][1000 genomes]
rs3936065	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4718325	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4718335	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4718346	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4718348	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6460276	0.82[EUR][1000 genomes]
rs6460281	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6460298	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6460302	0.82[YRI][hapmap]
rs6460304	0.82[YRI][hapmap]
rs66594357	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67775320	0.89[EUR][1000 genomes]
rs6945896	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6947339	0.82[YRI][hapmap]
rs6950988	0.85[EUR][1000 genomes]
rs6960848	0.89[EUR][1000 genomes]
rs6962717	0.82[YRI][hapmap]
rs6969224	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6970498	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6979636	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73142233	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73142245	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73142265	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73146609	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73148639	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73148689	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs73150604	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73152714	0.83[EUR][1000 genomes]
rs73376394	0.80[EUR][1000 genomes]
rs73376401	0.81[EUR][1000 genomes]
rs7782212	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7783889	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7785117	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7786735	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs778697	0.82[YRI][hapmap]
rs778711	0.82[YRI][hapmap]
rs778720	0.84[YRI][hapmap]
rs778736	0.82[YRI][hapmap]
rs7801332	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7810213	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7811204	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1909508	GUSB	cis	parietal	SCAN
rs1909508	RNU6-96P	cis	Thyroid	GTEx
rs1909508	ERV3	cis	multi-tissue	Pritchard
rs1909508	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs1909508	GS1-124K5.4	cis	Stomach	GTEx
rs1909508	GS1-124K5.4	cis	Artery Aorta	GTEx
rs1909508	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs1909508	TPST1	cis	multi-tissue	Pritchard
rs1909508	ZNF273	cis	cerebellum	SCAN
rs1909508	ZNF92	cis	parietal	SCAN
rs1909508	RABGEF1	cis	cerebellum	SCAN
rs1909508	GTF2IRD1P1	cis	Thyroid	GTEx
rs1909508	RABGEF1	cis	parietal	SCAN
rs1909508	GS1-124K5.11	cis	Thyroid	GTEx
rs1909508	VKORC1L1	cis	multi-tissue	Pritchard

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65747800-65766600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr7:65761000-65768600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr7:65761600-65772400	Weak transcription	HSMM	muscle
4	chr7:65762600-65768800	Weak transcription	NHLF	lung
5	chr7:65762800-65768000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr7:65763000-65768200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr7:65763000-65769200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr7:65763000-65770400	Weak transcription	HepG2	liver
9	chr7:65763000-65786200	Weak transcription	Primary B cells from cord blood	blood
10	chr7:65763200-65768200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr7:65763200-65768200	Weak transcription	NHEK	skin
12	chr7:65763200-65768800	Weak transcription	HMEC	breast
13	chr7:65763800-65766400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr7:65763800-65769400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:65764200-65767000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr7:65764200-65767800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr7:65764400-65767400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr7:65764600-65767400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:65765200-65768000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr7:65765400-65767800	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr7:65765600-65766400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr7:65765600-65766600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr7:65765800-65768800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:65766000-65767000	Enhancers	HUES48 Cell Line	embryonic stem cell
25	chr7:65766200-65766600	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr7:65766200-65766600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr7:65766200-65768200	Enhancers	iPS-20b Cell Line	embryonic stem cell

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