Variant report

Variant	rs2590379
Chromosome Location	chr10:49571720-49571721
allele	A/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:49571283..49571906-chr10:49652430..49653469,3	MCF-7	breast:
2	chr10:49570710..49573542-chr10:49731665..49733795,2	K562	blood:
3	chr10:49571219..49572252-chr10:49713441..49714210,3	MCF-7	breast:
4	chr10:49571674..49573268-chr10:49594315..49596996,2	K562	blood:
5	chr10:49571307..49572098-chr10:49717849..49718757,3	MCF-7	breast:
6	chr10:49570787..49573176-chr10:49651060..49654395,3	MCF-7	breast:
7	chr10:49571458..49572711-chr10:49713545..49714151,3	MCF-7	breast:
8	chr10:49571485..49572253-chr10:49714436..49715142,2	MCF-7	breast:
9	chr10:49571331..49572802-chr10:49714283..49715560,20	K562	blood:
10	chr10:49571319..49572300-chr10:49717652..49718657,4	MCF-7	breast:
11	chr10:49571145..49574084-chr10:49715215..49717894,2	MCF-7	breast:
12	chr10:49571331..49572227-chr10:49731692..49732606,3	K562	blood:
13	chr10:49571202..49572251-chr10:49863994..49864953,8	K562	blood:
14	chr10:49571231..49572227-chr10:49652604..49653258,3	MCF-7	breast:
15	chr10:49571375..49572211-chr10:49714319..49715238,7	MCF-7	breast:
16	chr10:49569844..49571916-chr17:59471462..59473939,2	MCF-7	breast:
17	chr10:49570196..49573404-chr10:49729951..49734102,5	K562	blood:

No data

Variant related genes	Relation type
ENSG00000128805	Chromatin interaction
ENSG00000267280	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10735224	0.87[AFR][1000 genomes]
rs10735225	0.87[AFR][1000 genomes]
rs10776599	0.87[AFR][1000 genomes]
rs10857567	1.00[CEU][hapmap]
rs11101265	1.00[CEU][hapmap]
rs11816450	1.00[CEU][hapmap]
rs12249536	1.00[CEU][hapmap]
rs12252237	1.00[CEU][hapmap]
rs1429801	1.00[CEU][hapmap]
rs1429802	1.00[CEU][hapmap]
rs1542153	1.00[EUR][1000 genomes]
rs1550774	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1623017	1.00[CEU][hapmap]
rs17011328	1.00[CEU][hapmap]
rs1881739	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1919705	0.92[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1978998	1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2463956	0.86[AFR][1000 genomes]
rs2590380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2590387	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2590388	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs2590390	0.92[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2698760	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2698765	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2698769	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs3730154	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41301111	1.00[EUR][1000 genomes]
rs4141840	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58181014	0.89[AFR][1000 genomes]
rs59377405	1.00[EUR][1000 genomes]
rs60467447	1.00[EUR][1000 genomes]
rs61343950	1.00[EUR][1000 genomes]
rs7072065	1.00[EUR][1000 genomes]
rs7073628	1.00[EUR][1000 genomes]
rs7085678	1.00[YRI][hapmap];0.94[AFR][1000 genomes]
rs7098618	1.00[CEU][hapmap]
rs73293121	1.00[EUR][1000 genomes]
rs73293181	0.83[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73293198	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73298383	1.00[EUR][1000 genomes]
rs73300395	1.00[EUR][1000 genomes]
rs74130210	0.83[EUR][1000 genomes]
rs74130216	1.00[EUR][1000 genomes]
rs7894863	0.87[AFR][1000 genomes]
rs7901179	1.00[EUR][1000 genomes]
rs7915014	1.00[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv895366	chr10:49299274-49576454	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv467190	chr10:49402084-49576878	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv550811	chr10:49402084-49576878	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
5	nsv6587	chr10:49526329-49571804	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49543000-49576200	Weak transcription	Right Atrium	heart
2	chr10:49559600-49572000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr10:49563600-49572000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr10:49566000-49571800	Weak transcription	Adipose Nuclei	Adipose
5	chr10:49566000-49573200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr10:49566400-49580000	Weak transcription	Colon Smooth Muscle	Colon
7	chr10:49566800-49571800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:49568200-49573000	Weak transcription	Brain Anterior Caudate	brain
9	chr10:49568600-49582000	Weak transcription	Psoas Muscle	Psoas
10	chr10:49568800-49571800	Weak transcription	Brain Angular Gyrus	brain
11	chr10:49568800-49571800	Weak transcription	NHLF	lung
12	chr10:49568800-49572000	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr10:49568800-49573200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr10:49568800-49576400	Weak transcription	Ovary	ovary
15	chr10:49569000-49572000	Enhancers	Fetal Heart	heart
16	chr10:49569400-49571800	Weak transcription	NHDF-Ad	bronchial
17	chr10:49569400-49573000	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr10:49569400-49574400	Weak transcription	Rectal Smooth Muscle	rectum
19	chr10:49569600-49571800	Weak transcription	HSMM	muscle
20	chr10:49569800-49571800	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr10:49570200-49571800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr10:49570200-49571800	Weak transcription	Fetal Lung	lung
23	chr10:49570400-49571800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr10:49570400-49571800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr10:49571000-49572600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr10:49571200-49573600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:49571200-49573600	Enhancers	Liver	Liver
28	chr10:49571200-49573600	Enhancers	K562	blood
29	chr10:49571200-49574600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr10:49571400-49571800	Enhancers	A549	lung
31	chr10:49571400-49571800	Enhancers	HUVEC	blood vessel
32	chr10:49571600-49571800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr10:49571600-49571800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:49571600-49573200	Enhancers	iPS-18 Cell Line	embryonic stem cell

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