Variant report

Variant	rs6990116
Chromosome Location	chr8:9577096-9577097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr8:9576896-9577448	SK-N-SH	brain:	n/a	chr8:9577218-9577225 chr8:9577218-9577225 chr8:9577218-9577225
2	GATA3	chr8:9576924-9577472	SK-N-SH	brain:	n/a	chr8:9577218-9577225 chr8:9577218-9577225 chr8:9577218-9577225

Variant related genes	Relation type
TNKS	TF binding region

Extended variants
information (count: 106 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs10086535	0.88[EUR][1000 genomes]
rs10090277	1.00[CEU][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes]
rs10090998	0.92[EUR][1000 genomes]
rs10090999	0.92[EUR][1000 genomes]
rs10093972	0.87[CEU][hapmap];0.94[GIH][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs10105767	0.87[CEU][hapmap];0.90[EUR][1000 genomes]
rs10105968	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs11249940	0.94[EUR][1000 genomes]
rs11249944	0.87[CEU][hapmap];0.96[EUR][1000 genomes]
rs11984920	0.97[GIH][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs11988208	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes]
rs11991831	0.91[EUR][1000 genomes]
rs11995167	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.94[EUR][1000 genomes]
rs12056794	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[TSI][hapmap];0.86[EUR][1000 genomes]
rs12234900	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs12234999	1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes]
rs12235001	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs28495967	0.86[EUR][1000 genomes]
rs28499425	0.90[EUR][1000 genomes]
rs28562614	0.92[EUR][1000 genomes]
rs28675389	0.94[EUR][1000 genomes]
rs3209608	0.87[EUR][1000 genomes]
rs33944167	0.96[EUR][1000 genomes]
rs34614689	0.94[EUR][1000 genomes]
rs35052906	0.98[EUR][1000 genomes]
rs35420737	0.90[EUR][1000 genomes]
rs35721526	0.90[EUR][1000 genomes]
rs36036709	0.94[EUR][1000 genomes]
rs4319098	0.87[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs4348499	0.90[EUR][1000 genomes]
rs4380943	0.87[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes]
rs4383973	0.87[CEU][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs4474027	0.87[CEU][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4529464	0.84[EUR][1000 genomes]
rs4612344	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs4629869	0.87[CEU][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs4841215	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[GIH][hapmap];0.90[TSI][hapmap]
rs5002814	0.88[EUR][1000 genomes]
rs5002815	0.87[CEU][hapmap];0.87[GIH][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes]
rs5018578	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs55924085	0.92[EUR][1000 genomes]
rs57000316	0.88[EUR][1000 genomes]
rs57024674	0.88[EUR][1000 genomes]
rs57331392	0.92[EUR][1000 genomes]
rs57482128	0.94[EUR][1000 genomes]
rs57580633	0.90[EUR][1000 genomes]
rs57987233	0.94[EUR][1000 genomes]
rs58458097	0.92[EUR][1000 genomes]
rs58596872	0.98[EUR][1000 genomes]
rs59201801	0.90[EUR][1000 genomes]
rs59268701	0.92[EUR][1000 genomes]
rs59519630	0.88[EUR][1000 genomes]
rs59940446	0.88[EUR][1000 genomes]
rs60051555	0.92[EUR][1000 genomes]
rs60078276	0.94[EUR][1000 genomes]
rs60222666	0.98[EUR][1000 genomes]
rs60801852	0.91[EUR][1000 genomes]
rs60857446	0.91[EUR][1000 genomes]
rs60942347	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61594550	0.92[EUR][1000 genomes]
rs61682841	0.90[EUR][1000 genomes]
rs6422356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.80[MKK][hapmap];0.90[TSI][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6601358	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6981763	0.88[EUR][1000 genomes]
rs6984737	0.87[CEU][hapmap];0.87[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs6985140	0.87[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6986755	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs6987259	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.94[EUR][1000 genomes]
rs6987746	0.90[EUR][1000 genomes]
rs6992432	0.88[GIH][hapmap]
rs6994452	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6995292	1.00[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.91[EUR][1000 genomes]
rs7000182	0.86[EUR][1000 genomes]
rs7001395	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7002917	0.87[CEU][hapmap];0.90[GIH][hapmap];0.81[TSI][hapmap];0.88[EUR][1000 genomes]
rs7009596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7010154	1.00[CEU][hapmap];0.85[CHB][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs7014218	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7016632	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7018268	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs7018348	0.86[EUR][1000 genomes]
rs73523222	0.86[EUR][1000 genomes]
rs73523224	0.90[EUR][1000 genomes]
rs73523249	0.92[EUR][1000 genomes]
rs73535828	0.86[EUR][1000 genomes]
rs73537955	0.88[EUR][1000 genomes]
rs73537959	0.86[EUR][1000 genomes]
rs73537971	0.88[EUR][1000 genomes]
rs73539904	0.90[EUR][1000 genomes]
rs73539907	0.90[EUR][1000 genomes]
rs73662516	0.88[EUR][1000 genomes]
rs7813518	0.91[EUR][1000 genomes]
rs7815297	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7815378	0.86[EUR][1000 genomes]
rs7815506	0.90[EUR][1000 genomes]
rs7815644	0.88[EUR][1000 genomes]
rs7818016	0.86[EUR][1000 genomes]
rs7821007	0.90[EUR][1000 genomes]
rs7827395	0.94[EUR][1000 genomes]
rs7837344	0.90[EUR][1000 genomes]
rs7837923	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs7840161	0.92[EUR][1000 genomes]
rs7846023	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs9644705	0.91[EUR][1000 genomes]
rs9644706	0.91[EUR][1000 genomes];0.98[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

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:9513400-9605400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr8:9529600-9606400	Weak transcription	Esophagus	oesophagus
3	chr8:9535000-9608000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr8:9537600-9592400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr8:9541400-9592200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:9542200-9606800	Weak transcription	Small Intestine	intestine
7	chr8:9543000-9592200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr8:9543400-9606400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr8:9544000-9586200	Weak transcription	Thymus	Thymus
10	chr8:9544000-9592400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr8:9544000-9592400	Weak transcription	Psoas Muscle	Psoas
12	chr8:9545600-9592400	Weak transcription	Brain Angular Gyrus	brain
13	chr8:9548400-9584400	Weak transcription	Hela-S3	cervix
14	chr8:9550000-9627600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr8:9551000-9592400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:9551200-9610600	Weak transcription	Fetal Brain Male	brain
17	chr8:9555400-9586400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr8:9557400-9632200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr8:9558000-9592400	Weak transcription	Gastric	stomach
20	chr8:9558400-9597600	Weak transcription	Spleen	Spleen
21	chr8:9558400-9605000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr8:9559400-9592400	Weak transcription	Right Ventricle	heart
23	chr8:9560600-9609200	Weak transcription	K562	blood
24	chr8:9561000-9616200	Weak transcription	Brain Substantia Nigra	brain
25	chr8:9561400-9592000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr8:9562200-9577800	Weak transcription	Lung	lung
27	chr8:9562200-9608000	Weak transcription	Colon Smooth Muscle	Colon
28	chr8:9562600-9592400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr8:9562800-9592400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr8:9564000-9608200	Weak transcription	Colonic Mucosa	Colon
31	chr8:9565000-9577800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr8:9565000-9606400	Weak transcription	Rectal Smooth Muscle	rectum
33	chr8:9565000-9608000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr8:9565000-9616200	Weak transcription	Pancreas	Pancrea
35	chr8:9565400-9592400	Weak transcription	HUVEC	blood vessel
36	chr8:9565600-9577800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr8:9565800-9577800	Weak transcription	Fetal Kidney	kidney
38	chr8:9566000-9577600	Weak transcription	HMEC	breast
39	chr8:9566000-9639400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr8:9567800-9577600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr8:9567800-9577800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr8:9567800-9592000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
43	chr8:9567800-9605400	Weak transcription	NHLF	lung
44	chr8:9567800-9611200	Weak transcription	NHEK	skin
45	chr8:9568000-9577800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr8:9568000-9583600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr8:9568000-9592400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr8:9568200-9578000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr8:9568800-9577800	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr8:9569000-9588400	Weak transcription	NHDF-Ad	bronchial

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