Variant report

Variant	rs9378980
Chromosome Location	chr6:5684890-5684891
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:5678900..5683178-chr6:5683336..5687695,5	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1001568	0.84[CHB][hapmap]
rs11752777	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.87[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13213128	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2005970	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2142738	0.82[CEU][hapmap];0.90[CHB][hapmap];0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs2326634	0.85[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs4140654	0.81[CHB][hapmap]
rs4959347	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4960125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4960126	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58316826	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62385480	0.81[ASN][1000 genomes]
rs62408067	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6918561	0.81[CHB][hapmap]
rs6918675	0.80[CHB][hapmap]
rs760675	0.90[CHB][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap]
rs7739358	0.84[CHB][hapmap];0.83[JPT][hapmap]
rs7746913	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs877010	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs878988	0.81[CHB][hapmap]
rs9328328	0.82[CHB][hapmap]
rs9378979	0.81[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.80[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9378983	0.80[CHB][hapmap]
rs9392709	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9392710	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9405278	0.80[ASN][1000 genomes]
rs9405280	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9405281	0.88[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];0.89[JPT][hapmap];0.85[TSI][hapmap];0.87[EUR][1000 genomes]
rs9405859	0.85[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9405861	0.95[CHB][hapmap];0.84[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9504488	0.85[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916361	chr6:5315853-5695486	Weak transcription Enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv600887	chr6:5545046-5694713	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:5672200-5705800	Weak transcription	Thymus	Thymus
2	chr6:5672400-5685600	Weak transcription	Aorta	Aorta
3	chr6:5673800-5701200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr6:5673800-5709800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr6:5678000-5686200	Weak transcription	Gastric	stomach
6	chr6:5678000-5709400	Weak transcription	Pancreas	Pancrea
7	chr6:5678200-5694000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:5678400-5693400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr6:5678600-5686600	Weak transcription	Right Atrium	heart
10	chr6:5680600-5695400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr6:5680800-5687600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:5680800-5695000	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr6:5681800-5695000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr6:5682200-5693200	Weak transcription	Primary T cells from cord blood	blood
15	chr6:5682400-5695200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:5682400-5695400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr6:5683800-5685200	Weak transcription	Fetal Intestine Small	intestine
18	chr6:5684400-5685000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:5684400-5685000	Enhancers	HSMMtube	muscle
20	chr6:5684400-5685200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:5684400-5685200	Enhancers	Muscle Satellite Cultured Cells	--
22	chr6:5684400-5685200	Enhancers	Osteobl	bone
23	chr6:5684400-5685400	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:5684400-5685800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:5684600-5695400	Weak transcription	Fetal Stomach	stomach
26	chr6:5684800-5696000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr6:5684800-5706000	Weak transcription	Ovary	ovary

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