Variant report

Variant	rs16896564
Chromosome Location	chr8:99032925-99032926
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	chr8:99032588-99032991	T-47D	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr8:99024327..99027909-chr8:99029199..99033016,4	MCF-7	breast:

Variant related genes	Relation type
MATN2	TF binding region

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10090458	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10955143	0.81[JPT][hapmap]
rs11994638	1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12375372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12674810	1.00[CEU][hapmap];0.89[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12675608	1.00[AFR][1000 genomes]
rs12680911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13270713	0.81[JPT][hapmap]
rs1378121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16892217	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16896467	1.00[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16896468	1.00[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs16896471	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs16896476	1.00[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs16896503	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16896514	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16896518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16896521	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs16896531	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16896600	1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1869607	1.00[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1961270	0.82[CHB][hapmap];0.89[JPT][hapmap];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2010014	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2045805	1.00[AFR][1000 genomes]
rs2045807	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs2061053	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2290473	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2513844	1.00[CEU][hapmap]
rs34354078	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4734381	1.00[CEU][hapmap];0.82[CHB][hapmap];0.89[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4735516	1.00[CEU][hapmap];0.93[MEX][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes]
rs4735519	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59704264	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs60346298	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60580631	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6980810	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs6988458	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7010226	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7018411	0.82[EUR][1000 genomes]
rs72677062	1.00[AFR][1000 genomes]
rs72677085	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs72677098	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs72678728	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72678733	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72678734	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72678737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72678752	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72678755	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs72678761	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs72678762	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7830701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7843262	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.87[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99008400-99045000	Weak transcription	Colonic Mucosa	Colon
2	chr8:99015000-99034400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
3	chr8:99019000-99033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr8:99020000-99033400	Weak transcription	Left Ventricle	heart
5	chr8:99021200-99053600	Weak transcription	A549	lung
6	chr8:99021400-99033400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr8:99021400-99043800	Weak transcription	Brain Germinal Matrix	brain
8	chr8:99022400-99055200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr8:99023000-99033400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr8:99023600-99034800	Strong transcription	Placenta Amnion	Placenta Amnion
11	chr8:99023800-99041200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr8:99024000-99044000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr8:99024000-99054800	Weak transcription	Right Ventricle	heart
14	chr8:99024200-99033200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr8:99024200-99033200	Weak transcription	NHDF-Ad	bronchial
16	chr8:99024200-99033600	Weak transcription	Rectal Smooth Muscle	rectum
17	chr8:99024200-99042800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr8:99024200-99055000	Weak transcription	Fetal Brain Male	brain
19	chr8:99024200-99056000	Weak transcription	Spleen	Spleen
20	chr8:99025000-99052800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr8:99025200-99045400	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr8:99025400-99045200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr8:99026000-99033200	Weak transcription	NHLF	lung
24	chr8:99026800-99033400	Weak transcription	Small Intestine	intestine
25	chr8:99026800-99036600	Weak transcription	Lung	lung
26	chr8:99027600-99037400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr8:99027600-99045400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr8:99028400-99033400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr8:99028800-99045400	Weak transcription	Fetal Brain Female	brain
30	chr8:99029000-99053600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr8:99029200-99033400	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr8:99030000-99045000	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr8:99030000-99045200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr8:99030400-99033200	Weak transcription	Adipose Nuclei	Adipose
35	chr8:99030400-99036800	Weak transcription	Osteobl	bone
36	chr8:99030400-99037400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr8:99030400-99043200	Weak transcription	Esophagus	oesophagus
38	chr8:99030600-99033000	Weak transcription	Brain Anterior Caudate	brain
39	chr8:99030600-99033400	Weak transcription	Brain Angular Gyrus	brain
40	chr8:99030600-99036600	Weak transcription	Primary T cells from cord blood	blood
41	chr8:99030600-99036600	Weak transcription	Fetal Intestine Large	intestine
42	chr8:99030600-99042600	Weak transcription	Placenta	Placenta
43	chr8:99030600-99053400	Weak transcription	Pancreas	Pancrea
44	chr8:99030600-99056800	Weak transcription	Aorta	Aorta
45	chr8:99030800-99033000	Weak transcription	Stomach Smooth Muscle	stomach
46	chr8:99030800-99033400	Weak transcription	Brain Hippocampus Middle	brain
47	chr8:99030800-99036800	Weak transcription	Primary B cells from cord blood	blood
48	chr8:99030800-99046400	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr8:99031000-99033000	Weak transcription	Duodenum Mucosa	Duodenum
50	chr8:99031000-99033000	Weak transcription	Fetal Kidney	kidney

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