Variant report

Variant	rs12470190
Chromosome Location	chr2:152630693-152630694
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:152629488..152631767-chr2:152636372..152638512,2	MCF-7	breast:
2	chr2:152621355..152624044-chr2:152629210..152631031,2	K562	blood:
3	chr2:152563836..152565601-chr2:152630541..152632941,2	K562	blood:
4	chr2:152627660..152631173-chr2:152633885..152636824,5	K562	blood:
5	chr2:152623627..152626142-chr2:152629148..152631495,3	K562	blood:
6	chr2:152626208..152631053-chr2:152637022..152639417,4	K562	blood:
7	chr2:152630249..152631929-chr2:152665981..152667860,2	K562	blood:
8	chr2:152630565..152634239-chr2:152680606..152685047,4	K562	blood:
9	chr2:152616288..152619244-chr2:152629461..152632128,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000162980	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10171724	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10180065	0.90[ASN][1000 genomes]
rs10184063	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10198530	0.91[ASN][1000 genomes]
rs10198531	0.93[ASN][1000 genomes]
rs10754989	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11682909	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11894672	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11896217	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12472627	0.97[ASN][1000 genomes]
rs12693116	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1523181	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1916301	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1916302	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030588	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2293221	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3768658	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3922996	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3922997	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4233654	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4306714	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4393745	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4414677	0.90[ASN][1000 genomes]
rs4450595	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4510224	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4552188	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4605370	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4664066	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433590	0.83[ASN][1000 genomes]
rs6715027	0.90[ASN][1000 genomes]
rs6715607	0.84[ASN][1000 genomes]
rs6718439	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6740508	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7557801	0.83[ASN][1000 genomes]
rs7564630	0.90[ASN][1000 genomes]
rs7580820	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7581532	0.87[ASN][1000 genomes]
rs7583060	0.90[ASN][1000 genomes]
rs7583148	0.90[ASN][1000 genomes]
rs7592798	0.96[ASN][1000 genomes]
rs9287998	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9288006	1.00[EUR][1000 genomes];0.94[ASN][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	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:89 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152611000-152632400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:152614600-152638000	Weak transcription	Pancreas	Pancrea
3	chr2:152616800-152644400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:152616800-152662400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr2:152617000-152632600	Weak transcription	Brain Hippocampus Middle	brain
6	chr2:152617000-152638000	Weak transcription	Esophagus	oesophagus
7	chr2:152617000-152669400	Weak transcription	Gastric	stomach
8	chr2:152618200-152631200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:152619000-152677400	Weak transcription	Brain Substantia Nigra	brain
10	chr2:152619800-152635800	Weak transcription	Fetal Brain Female	brain
11	chr2:152620200-152632000	Enhancers	Primary B cells from cord blood	blood
12	chr2:152622000-152632800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr2:152622000-152632800	Weak transcription	Thymus	Thymus
14	chr2:152622200-152632200	Weak transcription	Fetal Intestine Large	intestine
15	chr2:152622200-152661800	Weak transcription	Fetal Kidney	kidney
16	chr2:152622600-152633000	Weak transcription	Right Ventricle	heart
17	chr2:152622600-152633800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr2:152623000-152680000	Weak transcription	Spleen	Spleen
19	chr2:152623200-152638000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:152623400-152631800	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:152623400-152632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr2:152623400-152632600	Weak transcription	Fetal Thymus	thymus
23	chr2:152623400-152635800	Weak transcription	Primary hematopoietic stem cells	blood
24	chr2:152623400-152658800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:152623400-152659000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr2:152623600-152633800	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr2:152623600-152659000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr2:152623800-152631600	Weak transcription	Lung	lung
29	chr2:152623800-152633600	Weak transcription	Fetal Intestine Small	intestine
30	chr2:152623800-152635800	Weak transcription	Brain Anterior Caudate	brain
31	chr2:152623800-152642000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:152624000-152633400	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr2:152624000-152662600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:152624200-152632200	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr2:152624200-152632200	Weak transcription	Left Ventricle	heart
36	chr2:152624200-152632400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
37	chr2:152624200-152632400	Weak transcription	Fetal Muscle Trunk	muscle
38	chr2:152624200-152633400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr2:152624200-152641400	Weak transcription	Brain Angular Gyrus	brain
40	chr2:152624200-152643000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr2:152624400-152631400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr2:152624400-152635800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:152624400-152656800	Weak transcription	HepG2	liver
44	chr2:152625400-152660000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr2:152625600-152632600	Weak transcription	Ovary	ovary
46	chr2:152626200-152632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr2:152626800-152633600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr2:152626800-152643600	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr2:152626800-152647000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr2:152627000-152632200	Weak transcription	Sigmoid Colon	Sigmoid Colon

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