Variant report

Variant	rs6992589
Chromosome Location	chr8:117795185-117795186
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	chr8:117784066..117787028-chr8:117794164..117796661,2	MCF-7	breast:

Extended variants
information (count: 60 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10089815	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10094452	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10095889	0.85[ASN][1000 genomes]
rs10104144	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10109369	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10283122	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10283129	0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs10505284	0.83[ASN][1000 genomes]
rs10808485	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11775890	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs11776214	0.82[ASN][1000 genomes]
rs11781754	0.83[ASN][1000 genomes]
rs11783824	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12546186	0.83[ASN][1000 genomes]
rs12548402	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12675074	0.88[ASN][1000 genomes]
rs12675093	0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs13250873	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13258789	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13266314	0.92[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs13268448	0.82[ASN][1000 genomes]
rs1374299	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1436767	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs17664079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1867841	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2121339	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34672734	0.87[ASN][1000 genomes]
rs34701891	0.89[ASN][1000 genomes]
rs35682273	0.87[ASN][1000 genomes]
rs4372028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4449824	1.00[CEU][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4464999	0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4514005	0.87[ASN][1000 genomes]
rs4532623	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4876365	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4876671	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4876672	0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4876675	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4876679	0.81[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4876680	0.87[ASN][1000 genomes]
rs62510194	0.81[ASN][1000 genomes]
rs6469659	0.84[CEU][hapmap];0.88[TSI][hapmap]
rs6469660	0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs6981932	0.82[ASN][1000 genomes]
rs6983034	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6988190	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6990665	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7006087	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7013007	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7014156	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7814084	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7817878	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7823870	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7828774	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7836226	0.87[ASN][1000 genomes]
rs7843792	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[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	nsv530386	chr8:117509968-118391406	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv831434	chr8:117784467-117977825	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1027259	chr8:117790928-117842055	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv1034015	chr8:117790928-117843979	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6992589	MRPL13	cis	parietal	SCAN
rs6992589	C8orf53	cis	multi-tissue	Pritchard

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:117780000-117795600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr8:117780400-117795200	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr8:117780400-117796000	Weak transcription	Lung	lung
4	chr8:117780400-117798800	Weak transcription	HSMMtube	muscle
5	chr8:117780400-117799800	Weak transcription	Fetal Stomach	stomach
6	chr8:117780400-117830200	Weak transcription	Aorta	Aorta
7	chr8:117780600-117796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr8:117780600-117800600	Weak transcription	Colon Smooth Muscle	Colon
9	chr8:117780600-117800600	Weak transcription	Psoas Muscle	Psoas
10	chr8:117780600-117800800	Weak transcription	Brain Angular Gyrus	brain
11	chr8:117780600-117800800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr8:117780600-117800800	Weak transcription	Brain Substantia Nigra	brain
13	chr8:117780600-117802200	Weak transcription	Brain Cingulate Gyrus	brain
14	chr8:117782000-117814000	Weak transcription	Ovary	ovary
15	chr8:117783400-117796800	Weak transcription	HMEC	breast
16	chr8:117784000-117795800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr8:117784000-117796000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr8:117784000-117800600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr8:117784400-117800800	Weak transcription	Fetal Lung	lung
20	chr8:117784600-117800400	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr8:117784600-117804800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr8:117784800-117798800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr8:117785400-117795200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr8:117785400-117795600	Weak transcription	HUES6 Cell Line	embryonic stem cell
25	chr8:117785400-117795800	Weak transcription	Fetal Brain Male	brain
26	chr8:117785400-117800600	Weak transcription	Primary T helper cells fromperipheralblood	blood
27	chr8:117785400-117800800	Weak transcription	Liver	Liver
28	chr8:117785400-117800800	Weak transcription	Stomach Smooth Muscle	stomach
29	chr8:117785400-117801200	Weak transcription	Left Ventricle	heart
30	chr8:117785600-117796600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr8:117785600-117797200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr8:117785600-117798400	Weak transcription	GM12878-XiMat	blood
33	chr8:117785800-117795400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr8:117785800-117796200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr8:117785800-117800400	Weak transcription	Dnd41	blood
36	chr8:117786400-117800600	Weak transcription	Primary T cells fromperipheralblood	blood
37	chr8:117786400-117800600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr8:117786400-117800600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr8:117786600-117800800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr8:117786600-117800800	Weak transcription	Primary T cells from cord blood	blood
41	chr8:117786600-117800800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr8:117788200-117800800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr8:117790800-117797400	Weak transcription	HSMM	muscle
44	chr8:117792400-117795200	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr8:117792400-117795200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr8:117792600-117795200	Weak transcription	HUES64 Cell Line	embryonic stem cell
47	chr8:117792600-117795200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr8:117792600-117795800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr8:117793800-117795400	Weak transcription	Brain Anterior Caudate	brain
50	chr8:117793800-117800800	Weak transcription	Fetal Brain Female	brain

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