Variant report

Variant	rs6990300
Chromosome Location	chr8:9547861-9547862
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	chr8:9547745..9549765-chr8:9551335..9552928,2	K562	blood:

Extended variants
information (count: 66 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10081478	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10081565	1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10104032	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs10111376	0.86[CHB][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.81[ASN][1000 genomes]
rs10794712	0.80[CEU][hapmap]
rs10903317	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11249934	0.83[ASW][hapmap];0.98[GIH][hapmap]
rs11249937	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs11249942	0.80[CEU][hapmap]
rs11776236	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11779335	0.80[CEU][hapmap];0.90[MKK][hapmap]
rs12114182	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12114661	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12155819	0.83[ASW][hapmap];0.91[CHB][hapmap];0.95[GIH][hapmap];0.92[LWK][hapmap];0.97[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12541617	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12542457	0.82[ASW][hapmap];0.88[GIH][hapmap];0.93[LWK][hapmap];0.94[MKK][hapmap];0.82[AFR][1000 genomes]
rs12542912	0.91[CHB][hapmap]
rs12543959	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12544371	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12545912	0.80[MKK][hapmap]
rs12677313	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12679180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13250951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13260526	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13263409	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13264850	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs13270518	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13270801	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13272424	0.81[AMR][1000 genomes]
rs13273033	0.80[CEU][hapmap]
rs13276086	0.91[CHB][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.97[MKK][hapmap]
rs13282006	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1394	0.94[ASW][hapmap];0.98[GIH][hapmap];0.81[LWK][hapmap];0.80[MEX][hapmap];0.82[YRI][hapmap]
rs35316422	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4129360	0.91[CHB][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4240629	0.80[CEU][hapmap]
rs4313162	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4535744	0.80[CEU][hapmap]
rs4626603	0.84[CEU][hapmap]
rs4840426	0.83[ASW][hapmap];0.95[GIH][hapmap];0.80[MEX][hapmap]
rs4840434	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4840437	0.83[ASW][hapmap];0.81[GIH][hapmap];0.92[LWK][hapmap];0.96[MKK][hapmap];0.86[YRI][hapmap]
rs4841196	0.83[ASW][hapmap];1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4841212	0.80[CEU][hapmap]
rs6601327	0.85[MKK][hapmap]
rs6601340	0.84[MEX][hapmap]
rs6601344	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601350	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6982148	0.91[CHB][hapmap];0.86[YRI][hapmap]
rs6992666	0.82[ASN][1000 genomes]
rs6994574	0.91[CHB][hapmap];0.95[GIH][hapmap];0.80[LWK][hapmap];0.93[MKK][hapmap]
rs7003791	1.00[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7006985	0.82[AFR][1000 genomes]
rs7010270	0.80[CEU][hapmap]
rs7461376	0.80[CEU][hapmap]
rs7461939	0.91[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.84[ASN][1000 genomes]
rs7462070	0.84[ASN][1000 genomes]
rs7462910	0.80[CEU][hapmap];0.90[MKK][hapmap]
rs7822700	1.00[CEU][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7840706	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9644704	0.88[ASW][hapmap];0.90[GIH][hapmap];0.92[LWK][hapmap];0.93[MKK][hapmap];0.83[AFR][1000 genomes]
rs9644707	0.82[ASN][1000 genomes]
rs9644708	0.91[CHB][hapmap];0.84[CHD][hapmap]
rs9650638	0.80[CEU][hapmap]
rs9650639	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6990300	FLJ10661	cis	cerebellum	SCAN
rs6990300	MFHAS1	cis	cerebellum	SCAN
rs6990300	DEFB134	cis	cerebellum	SCAN
rs6990300	PRSS55	cis	cerebellum	SCAN
rs6990300	TNKS	cis	parietal	SCAN
rs6990300	CTSB	cis	cerebellum	SCAN
rs6990300	TNKS	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9504800-9549600	Weak transcription	Pancreas	Pancrea
2	chr8:9510400-9563800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr8:9511000-9564200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr8:9511600-9554600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr8:9512400-9551400	Weak transcription	Dnd41	blood
6	chr8:9513200-9564200	Weak transcription	Ovary	ovary
7	chr8:9513200-9567400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr8:9513400-9605400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr8:9513800-9563600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr8:9529600-9549000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr8:9529600-9606400	Weak transcription	Esophagus	oesophagus
12	chr8:9530600-9549400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr8:9530800-9549800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr8:9531200-9564000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr8:9534800-9563600	Weak transcription	HepG2	liver
16	chr8:9535000-9564800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr8:9535000-9608000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr8:9535400-9560800	Weak transcription	HMEC	breast
19	chr8:9535400-9563800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr8:9536400-9563400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr8:9537400-9549400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr8:9537400-9563600	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr8:9537600-9592400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr8:9539800-9549800	Weak transcription	Brain Germinal Matrix	brain
25	chr8:9540000-9565400	Weak transcription	Fetal Kidney	kidney
26	chr8:9541400-9592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr8:9541600-9563600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr8:9542200-9606800	Weak transcription	Small Intestine	intestine
29	chr8:9542400-9553400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr8:9543000-9592200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr8:9543400-9549400	Weak transcription	Duodenum Mucosa	Duodenum
32	chr8:9543400-9606400	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr8:9543600-9548000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr8:9543600-9550000	Strong transcription	Fetal Intestine Large	intestine
35	chr8:9543800-9550400	Weak transcription	Adipose Nuclei	Adipose
36	chr8:9543800-9563800	Weak transcription	Fetal Stomach	stomach
37	chr8:9543800-9564200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr8:9543800-9564200	Weak transcription	NH-A	brain
39	chr8:9544000-9549600	Weak transcription	GM12878-XiMat	blood
40	chr8:9544000-9562800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr8:9544000-9562800	Weak transcription	Left Ventricle	heart
42	chr8:9544000-9586200	Weak transcription	Thymus	Thymus
43	chr8:9544000-9592400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr8:9544000-9592400	Weak transcription	Psoas Muscle	Psoas
45	chr8:9544200-9571200	Weak transcription	Aorta	Aorta
46	chr8:9545000-9550600	Weak transcription	NHEK	skin
47	chr8:9545400-9548400	Weak transcription	A549	lung
48	chr8:9545400-9549600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr8:9545400-9560600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr8:9545400-9564400	Weak transcription	HSMM	muscle

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