Variant report

Variant	rs12004404
Chromosome Location	chr9:26984277-26984278
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10967605	0.84[EUR][1000 genomes]
rs12000194	0.81[EUR][1000 genomes]
rs12000403	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12000936	0.84[EUR][1000 genomes]
rs12001976	1.00[YRI][hapmap]
rs12002016	0.84[EUR][1000 genomes]
rs12002242	0.84[EUR][1000 genomes]
rs12002844	0.84[EUR][1000 genomes]
rs12002995	0.84[EUR][1000 genomes]
rs12003498	1.00[YRI][hapmap]
rs12003566	0.86[EUR][1000 genomes]
rs12004175	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12004792	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs12005943	0.84[EUR][1000 genomes]
rs12005959	0.84[EUR][1000 genomes]
rs13287000	0.88[AMR][1000 genomes]
rs16910907	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16910929	0.86[EUR][1000 genomes]
rs35138802	0.88[AMR][1000 genomes]
rs41271179	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs59452957	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60097289	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7043002	0.84[EUR][1000 genomes]
rs73643115	0.81[EUR][1000 genomes]
rs73643116	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528614	chr9:26893662-27074233	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv517269	chr9:26945976-27137242	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv892862	chr9:26956663-27190655	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:26957000-26984400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr9:26957000-27024000	Weak transcription	Esophagus	oesophagus
3	chr9:26957200-26984400	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr9:26957200-26984400	Weak transcription	Primary B cells from peripheral blood	blood
5	chr9:26957200-26984600	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:26957200-26984800	Weak transcription	Primary B cells from cord blood	blood
7	chr9:26957200-26984800	Weak transcription	Fetal Thymus	thymus
8	chr9:26957200-27026600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr9:26957200-27040000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr9:26957400-26984600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr9:26957600-26984800	Weak transcription	Brain Hippocampus Middle	brain
12	chr9:26957800-26984600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:26962200-26986400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr9:26962400-26984600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr9:26962400-26985000	Weak transcription	Brain Substantia Nigra	brain
16	chr9:26962600-26984600	Weak transcription	HSMM	muscle
17	chr9:26966400-26984600	Weak transcription	Fetal Brain Male	brain
18	chr9:26969000-26991200	Weak transcription	NHDF-Ad	bronchial
19	chr9:26969600-26986600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:26970800-26990000	Weak transcription	Spleen	Spleen
21	chr9:26972200-26986200	Weak transcription	Pancreas	Pancrea
22	chr9:26972200-26995000	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr9:26972800-26986800	Weak transcription	Aorta	Aorta
24	chr9:26972800-26990600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:26974200-26984400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr9:26974200-27023600	Weak transcription	Fetal Brain Female	brain
27	chr9:26975800-26984600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr9:26976200-26984600	Weak transcription	Placenta	Placenta
29	chr9:26976200-26984800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr9:26976200-27003600	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr9:26976600-26984600	Weak transcription	Right Ventricle	heart
32	chr9:26976600-26984800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr9:26976600-26985000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr9:26976600-26996800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr9:26976800-26984800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr9:26976800-26985000	Weak transcription	HSMMtube	muscle
37	chr9:26976800-26993000	Weak transcription	Osteobl	bone
38	chr9:26976800-27017800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr9:26977000-26984400	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr9:26977000-26984600	Weak transcription	A549	lung
41	chr9:26977000-26984800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr9:26977000-26984800	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr9:26977000-26986200	Weak transcription	HepG2	liver
44	chr9:26977000-26997000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr9:26977200-26984400	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr9:26977200-27019400	Weak transcription	NH-A	brain
47	chr9:26977400-26992200	Weak transcription	HMEC	breast
48	chr9:26977400-26994400	Weak transcription	NHEK	skin
49	chr9:26977400-26998600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr9:26977800-26996800	Weak transcription	H1 Cell Line	embryonic stem cell

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