Variant report

Variant	rs12669879
Chromosome Location	chr7:108036161-108036162
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	chr7:107936599..107939475-chr7:108034217..108037147,2	MCF-7	breast:

Extended variants
information (count: 70 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10245718	0.86[CEU][hapmap];0.81[AMR][1000 genomes]
rs11971972	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11973105	0.84[EUR][1000 genomes]
rs11973823	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11976021	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11979596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11983900	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12705470	0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs13222628	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13227836	0.85[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13228190	0.85[EUR][1000 genomes]
rs13238841	0.94[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs13245101	0.84[EUR][1000 genomes]
rs13245242	0.82[CEU][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs17155637	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap]
rs17338441	0.84[EUR][1000 genomes]
rs17338462	0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs17421351	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17423043	0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs17423119	0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs2108252	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2108253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2214913	0.84[EUR][1000 genomes]
rs2300036	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2300040	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2300048	0.85[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2300052	0.89[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs2395995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34218460	0.83[EUR][1000 genomes]
rs35429156	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35436957	0.85[EUR][1000 genomes]
rs35617326	0.84[EUR][1000 genomes]
rs56145857	0.84[EUR][1000 genomes]
rs59458537	0.85[EUR][1000 genomes]
rs60398019	0.83[EUR][1000 genomes]
rs6466224	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466225	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466226	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6466233	1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs66461825	0.84[EUR][1000 genomes]
rs67027479	0.84[EUR][1000 genomes]
rs6949637	0.84[EUR][1000 genomes]
rs6954366	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6959023	0.83[EUR][1000 genomes]
rs6959409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6960478	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6966107	0.95[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6967368	0.84[GIH][hapmap]
rs6969521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6976309	0.84[EUR][1000 genomes]
rs6976649	0.83[EUR][1000 genomes]
rs6976659	0.84[EUR][1000 genomes]
rs6976752	0.84[EUR][1000 genomes]
rs6976776	0.84[EUR][1000 genomes]
rs6976804	0.84[EUR][1000 genomes]
rs6978552	0.85[EUR][1000 genomes]
rs71213282	0.84[EUR][1000 genomes]
rs7784170	0.85[EUR][1000 genomes]
rs7786947	0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs7790875	0.94[GIH][hapmap];0.88[MEX][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs7792321	0.86[CHB][hapmap];0.83[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.83[ASN][1000 genomes]
rs7797885	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7806869	1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[EUR][1000 genomes]
rs7807737	0.84[EUR][1000 genomes]
rs7807941	0.84[EUR][1000 genomes]
rs9649307	0.84[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
2	nsv888942	chr7:107893695-108055858	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
3	nsv888943	chr7:107893695-108058574	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1030425	chr7:107910716-108041036	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12669879	PUS7	cis	parietal	SCAN
rs12669879	THAP5	Cis_1M	lymphoblastoid	RTeQTL
rs12669879	THAP5	cis	normal skin	skin_eQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108014800-108043200	Weak transcription	Brain Cingulate Gyrus	brain
2	chr7:108021400-108040800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr7:108021400-108043000	Weak transcription	HMEC	breast
4	chr7:108024000-108045600	Weak transcription	Brain Anterior Caudate	brain
5	chr7:108027800-108043000	Weak transcription	HUVEC	blood vessel
6	chr7:108033000-108041400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr7:108034200-108037000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr7:108034400-108037000	Enhancers	Fetal Brain Male	brain
9	chr7:108034600-108041400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr7:108034800-108038800	Strong transcription	A549	lung
11	chr7:108034800-108043000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr7:108035000-108046600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:108035400-108037000	Enhancers	Pancreatic Islets	Pancreatic Islet
14	chr7:108035800-108036200	Enhancers	Fetal Lung	lung
15	chr7:108035800-108036600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr7:108035800-108037000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr7:108036000-108036200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:108036000-108036400	Enhancers	Fetal Brain Female	brain
19	chr7:108036000-108036400	Enhancers	Spleen	Spleen
20	chr7:108036000-108036600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr7:108036000-108036600	Enhancers	Brain Angular Gyrus	brain
22	chr7:108036000-108036600	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
23	chr7:108036000-108036600	Enhancers	Brain Substantia Nigra	brain
24	chr7:108036000-108036600	Enhancers	Fetal Kidney	kidney
25	chr7:108036000-108036600	Enhancers	Pancreas	Pancrea
26	chr7:108036000-108037000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr7:108036000-108038000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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