Variant report

Variant	rs6469660
Chromosome Location	chr8:117797719-117797720
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:117795253..117798191-chr8:117798844..117800835,2	MCF-7	breast:
2	chr8:117777170..117780620-chr8:117796819..117800080,3	K562	blood:
3	chr8:117796423..117798926-chr8:117885716..117888098,2	MCF-7	breast:
4	chr8:117778305..117781180-chr8:117796959..117799544,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147679	Chromatin interaction
ENSG00000147677	Chromatin interaction
ENSG00000264875	Chromatin interaction
ENSG00000164754	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10094452	0.92[JPT][hapmap]
rs10095889	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10104144	0.83[ASN][1000 genomes]
rs10283122	0.85[CHB][hapmap];0.91[CHD][hapmap];0.84[ASN][1000 genomes]
rs10283129	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10808485	0.85[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs11783824	0.88[ASN][1000 genomes]
rs12548402	0.84[ASN][1000 genomes]
rs12675074	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12675093	0.94[ASW][hapmap];1.00[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];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13250873	0.89[ASN][1000 genomes]
rs13266314	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs1374299	0.92[ASN][1000 genomes]
rs1436767	0.91[CHD][hapmap];0.92[JPT][hapmap]
rs17664079	0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.85[ASN][1000 genomes]
rs1867841	0.91[ASN][1000 genomes]
rs2121339	0.85[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs34672734	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34701891	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35682273	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4145242	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4372028	0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.81[ASN][1000 genomes]
rs4449824	0.80[CHD][hapmap];0.92[JPT][hapmap]
rs4464999	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4514005	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4876365	0.90[ASN][1000 genomes]
rs4876679	1.00[CEU][hapmap];0.81[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4876680	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62510194	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6988190	0.86[ASN][1000 genomes]
rs6990665	0.83[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs6992589	0.85[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs7006087	0.89[ASN][1000 genomes]
rs7013007	0.89[ASN][1000 genomes]
rs7014156	0.85[CHB][hapmap];0.92[JPT][hapmap];0.92[ASN][1000 genomes]
rs7814084	0.85[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs7817878	0.91[ASN][1000 genomes]
rs7828774	0.92[ASN][1000 genomes]
rs7836226	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7843792	0.91[CHD][hapmap];0.92[JPT][hapmap]

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
rs6469660	EXT1	cis	cerebellum	SCAN
rs6469660	NOV	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:117780400-117798800	Weak transcription	HSMMtube	muscle
2	chr8:117780400-117799800	Weak transcription	Fetal Stomach	stomach
3	chr8:117780400-117830200	Weak transcription	Aorta	Aorta
4	chr8:117780600-117800600	Weak transcription	Colon Smooth Muscle	Colon
5	chr8:117780600-117800600	Weak transcription	Psoas Muscle	Psoas
6	chr8:117780600-117800800	Weak transcription	Brain Angular Gyrus	brain
7	chr8:117780600-117800800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr8:117780600-117800800	Weak transcription	Brain Substantia Nigra	brain
9	chr8:117780600-117802200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr8:117782000-117814000	Weak transcription	Ovary	ovary
11	chr8:117784000-117800600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr8:117784400-117800800	Weak transcription	Fetal Lung	lung
13	chr8:117784600-117800400	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr8:117784600-117804800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr8:117784800-117798800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr8:117785400-117800600	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr8:117785400-117800800	Weak transcription	Liver	Liver
18	chr8:117785400-117800800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr8:117785400-117801200	Weak transcription	Left Ventricle	heart
20	chr8:117785600-117798400	Weak transcription	GM12878-XiMat	blood
21	chr8:117785800-117800400	Weak transcription	Dnd41	blood
22	chr8:117786400-117800600	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr8:117786400-117800600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr8:117786400-117800600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr8:117786600-117800800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr8:117786600-117800800	Weak transcription	Primary T cells from cord blood	blood
27	chr8:117786600-117800800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr8:117788200-117800800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr8:117793800-117800800	Weak transcription	Fetal Brain Female	brain
30	chr8:117793800-117800800	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr8:117794000-117800400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr8:117794000-117800800	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr8:117796400-117800400	Weak transcription	HepG2	liver
34	chr8:117796600-117797800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr8:117796800-117797800	Enhancers	HMEC	breast
36	chr8:117797600-117800600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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