Variant report

Variant	rs12090365
Chromosome Location	chr1:9731858-9731859
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:9716614..9719394-chr1:9729879..9731950,2	K562	blood:
2	chr1:9730429..9733119-chr1:9735677..9738104,2	MCF-7	breast:
3	chr1:9728049..9730483-chr1:9731175..9733192,2	K562	blood:
4	chr1:9730384..9732236-chr1:9733949..9735646,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs12059589	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12064486	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12087498	0.94[AFR][1000 genomes]
rs12092982	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs28730677	1.00[GIH][hapmap]
rs72869688	0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7553125	1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3385337	chr1:9105242-10082223	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	549 gene(s)	inside rSNPs	diseases
2	nsv871610	chr1:9655795-10008221	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer 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	43 gene(s)	inside rSNPs	diseases
3	esv3417409	chr1:9683992-10241703	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv832203	chr1:9726632-9860209	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:9713200-9744000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr1:9713200-9747200	Weak transcription	Pancreas	Pancrea
3	chr1:9714000-9739600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr1:9718200-9734000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:9722400-9734600	Genic enhancers	Primary T cells fromperipheralblood	blood
6	chr1:9723600-9736800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:9724400-9734400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
8	chr1:9727200-9734600	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:9727200-9741000	Strong transcription	Dnd41	blood
10	chr1:9727800-9734600	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr1:9728000-9734400	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr1:9728200-9732800	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:9729000-9734200	Strong transcription	Primary B cells from cord blood	blood
14	chr1:9729600-9746800	Weak transcription	Thymus	Thymus
15	chr1:9730000-9733800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:9730400-9732200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr1:9730600-9734000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr1:9730600-9735000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr1:9730800-9732200	Strong transcription	Fetal Thymus	thymus
20	chr1:9730800-9734600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:9730800-9740000	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr1:9731000-9734400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr1:9731000-9734400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr1:9731000-9739600	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr1:9731200-9732200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr1:9731200-9732200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:9731200-9732200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:9731200-9732200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:9731200-9732200	Enhancers	HMEC	breast
30	chr1:9731200-9732200	Enhancers	HSMM	muscle
31	chr1:9731200-9732200	Enhancers	NH-A	brain
32	chr1:9731200-9732200	Enhancers	NHEK	skin
33	chr1:9731200-9732800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:9731200-9734400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
35	chr1:9731400-9732000	Enhancers	Muscle Satellite Cultured Cells	--
36	chr1:9731400-9732200	Enhancers	Lung	lung
37	chr1:9731400-9732400	Enhancers	A549	lung
38	chr1:9731400-9732600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:9731400-9733600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr1:9731600-9732000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:9731600-9732000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr1:9731600-9732000	Enhancers	HSMMtube	muscle
43	chr1:9731600-9732000	Enhancers	K562	blood
44	chr1:9731600-9732200	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr1:9731600-9732400	Genic enhancers	Primary T cells from cord blood	blood
46	chr1:9731600-9732400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
47	chr1:9731600-9733000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:9731800-9732200	Strong transcription	Spleen	Spleen
49	chr1:9731800-9732200	Flanking Bivalent TSS/Enh	HepG2	liver
50	chr1:9731800-9734400	Strong transcription	GM12878-XiMat	blood

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