Variant report

Variant	rs17138149
Chromosome Location	chr7:65693180-65693181
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:65680452..65683306-chr7:65691052..65694234,3	MCF-7	breast:
2	chr7:65692053..65693924-chr7:65696196..65697706,2	MCF-7	breast:

Extended variants
information (count: 93 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10261710	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10447522	0.82[YRI][hapmap]
rs1065265	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes]
rs10950024	0.83[ASN][1000 genomes]
rs10950025	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs10950026	1.00[CEU][hapmap]
rs10950027	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10950029	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950035	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10950036	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11760805	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11766183	0.91[EUR][1000 genomes]
rs11767262	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11767833	0.83[ASN][1000 genomes]
rs11769702	0.95[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11770063	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12666485	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12668269	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12670811	0.88[EUR][1000 genomes]
rs12671152	0.84[AMR][1000 genomes]
rs12671834	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12673308	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1547529	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs160641	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs1695820	0.82[YRI][hapmap]
rs17138089	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs17138156	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1909508	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]
rs2088655	0.82[YRI][hapmap]
rs2173571	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2279757	0.93[EUR][1000 genomes]
rs2420456	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2451953	0.87[ASN][1000 genomes]
rs2460427	0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2465121	0.86[ASN][1000 genomes]
rs28815324	0.80[ASN][1000 genomes]
rs313817	0.83[ASN][1000 genomes]
rs313818	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs313823	0.87[ASN][1000 genomes]
rs313829	0.87[CEU][hapmap];0.83[LWK][hapmap];0.89[TSI][hapmap];0.88[YRI][hapmap]
rs313830	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs316305	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs316306	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs316316	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs316320	0.85[ASN][1000 genomes]
rs316323	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.85[ASN][1000 genomes]
rs316324	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs316328	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.87[CHD][hapmap];0.92[GIH][hapmap];0.81[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs3936065	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4441996	0.86[ASN][1000 genomes]
rs4718325	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718335	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4718346	0.87[EUR][1000 genomes]
rs6460276	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6460281	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6460298	0.86[EUR][1000 genomes]
rs66594357	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67302640	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs67397473	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67688847	0.86[ASN][1000 genomes]
rs67775320	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6947339	0.82[YRI][hapmap]
rs6960870	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6962717	0.82[YRI][hapmap]
rs6969224	0.89[EUR][1000 genomes]
rs6970498	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6979636	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73136346	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs73142233	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73142245	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73142265	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73146609	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73148639	0.90[EUR][1000 genomes]
rs73148689	0.85[EUR][1000 genomes]
rs73376394	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73376401	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7782212	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7783727	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7783889	1.00[CEU][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7785117	0.92[EUR][1000 genomes]
rs7786728	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs7786735	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs778697	0.82[YRI][hapmap]
rs7787063	0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs778711	0.82[YRI][hapmap]
rs778720	0.84[YRI][hapmap]
rs778736	0.82[YRI][hapmap]
rs7801332	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7811204	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[EUR][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	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs17138149	RABGEF1	cis	cerebellum	SCAN
rs17138149	GS1-124K5.11	cis	Thyroid	GTEx
rs17138149	ERV3	cis	multi-tissue	Pritchard
rs17138149	GS1-124K5.4	cis	Stomach	GTEx
rs17138149	GUSB	cis	parietal	SCAN
rs17138149	RNU6-96P	cis	Thyroid	GTEx
rs17138149	VKORC1L1	cis	multi-tissue	Pritchard
rs17138149	RABGEF1	cis	parietal	SCAN
rs17138149	TPST1	cis	multi-tissue	Pritchard
rs17138149	ZNF273	cis	cerebellum	SCAN
rs17138149	GS1-124K5.4	cis	Artery Aorta	GTEx
rs17138149	GTF2IRD1P1	cis	Thyroid	GTEx
rs17138149	ZNF92	cis	parietal	SCAN
rs17138149	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs17138149	RP4-756H11.3	cis	Muscle Skeletal	GTEx

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
2	chr7:65676000-65696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
4	chr7:65676200-65696200	Weak transcription	Fetal Stomach	stomach
5	chr7:65676600-65693200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr7:65677000-65694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr7:65677200-65693800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr7:65685600-65696200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr7:65686800-65701600	Weak transcription	Osteobl	bone
10	chr7:65686800-65715400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr7:65687000-65701800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr7:65687000-65701800	Weak transcription	NHDF-Ad	bronchial
13	chr7:65687800-65701800	Weak transcription	Spleen	Spleen
14	chr7:65687800-65703400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr7:65689400-65703600	Weak transcription	NHLF	lung
16	chr7:65689600-65695800	Weak transcription	Brain Substantia Nigra	brain
17	chr7:65689600-65696200	Weak transcription	Lung	lung
18	chr7:65689600-65697800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr7:65689600-65701800	Weak transcription	Gastric	stomach
20	chr7:65689600-65715800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr7:65689800-65695000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr7:65689800-65695600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr7:65689800-65696200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr7:65689800-65697800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr7:65689800-65701800	Weak transcription	Fetal Lung	lung
26	chr7:65689800-65701800	Weak transcription	HMEC	breast
27	chr7:65689800-65702000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr7:65690000-65694400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr7:65690000-65698400	Weak transcription	Liver	Liver
30	chr7:65690200-65701800	Weak transcription	Ovary	ovary
31	chr7:65691200-65700200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr7:65692800-65693400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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