Variant report

Variant	rs2373532
Chromosome Location	chr2:39616029-39616030
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:39613589..39616397-chr2:39663811..39666348,2	K562	blood:
2	chr2:39613441..39616248-chr2:39657678..39659490,2	MCF-7	breast:
3	chr2:39609764..39613069-chr2:39616003..39618259,3	K562	blood:
4	chr2:39614635..39616169-chr2:39619014..39621210,2	MCF-7	breast:
5	chr2:39613765..39616642-chr2:39620557..39622902,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000011566	Chromatin interaction
ENSG00000231312	Chromatin interaction
ENSG00000252239	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10169501	0.85[ASN][1000 genomes]
rs10173722	0.84[ASN][1000 genomes]
rs10196447	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs10199459	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10199948	0.88[CHB][hapmap];0.81[JPT][hapmap]
rs11124683	0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11896389	0.91[EUR][1000 genomes]
rs12328714	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17023530	0.94[EUR][1000 genomes]
rs17023542	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17023547	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17023600	0.94[EUR][1000 genomes]
rs17023611	0.94[EUR][1000 genomes]
rs17023684	1.00[EUR][1000 genomes]
rs17023696	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17023773	0.97[EUR][1000 genomes]
rs17446102	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446515	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17446690	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs17505580	0.94[EUR][1000 genomes]
rs17505877	0.94[EUR][1000 genomes]
rs2056653	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2056655	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2111383	0.85[CEU][hapmap];1.00[EUR][1000 genomes]
rs2373530	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs3732052	1.00[EUR][1000 genomes]
rs3887311	0.96[YRI][hapmap]
rs4670273	0.85[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4670938	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55761128	1.00[EUR][1000 genomes]
rs6544227	0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6544229	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6720537	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6720951	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6721049	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6721740	0.97[EUR][1000 genomes]
rs6731310	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6758596	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73924009	1.00[EUR][1000 genomes]
rs7559436	1.00[EUR][1000 genomes]
rs7577097	0.82[CEU][hapmap];1.00[EUR][1000 genomes]
rs7588265	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7596222	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs7605939	0.82[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.97[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	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
2	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv997934	chr2:39473548-39751029	Enhancers Strong transcription ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39588000-39630400	Weak transcription	Placenta	Placenta
2	chr2:39591800-39621400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr2:39592800-39617600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:39603200-39638400	Weak transcription	Hela-S3	cervix
5	chr2:39603400-39625000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:39603400-39626800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:39607000-39626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:39607400-39624800	Weak transcription	Stomach Mucosa	stomach
9	chr2:39607600-39619800	Weak transcription	Primary hematopoietic stem cells	blood
10	chr2:39607600-39643400	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr2:39608000-39622800	Weak transcription	Fetal Kidney	kidney
12	chr2:39608400-39621000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr2:39608400-39626200	Weak transcription	Brain Substantia Nigra	brain
14	chr2:39609000-39617400	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:39609200-39617200	Weak transcription	NHDF-Ad	bronchial
16	chr2:39609200-39621600	Weak transcription	Lung	lung
17	chr2:39609400-39621200	Weak transcription	Brain Angular Gyrus	brain
18	chr2:39609400-39621200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr2:39609400-39621600	Weak transcription	HSMM	muscle
20	chr2:39609600-39617400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:39609600-39621200	Weak transcription	Brain Hippocampus Middle	brain
22	chr2:39609600-39621400	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr2:39609600-39621600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr2:39609600-39621600	Weak transcription	NH-A	brain
25	chr2:39609600-39621600	Weak transcription	Osteobl	bone
26	chr2:39609600-39626400	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr2:39610000-39621200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:39610200-39621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:39610200-39626400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
30	chr2:39610400-39617400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr2:39613000-39621400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr2:39613200-39618200	Enhancers	Colon Smooth Muscle	Colon
33	chr2:39613400-39621200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:39613600-39616400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:39613600-39621600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:39613600-39621600	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr2:39613800-39630600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:39614000-39619800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:39614000-39628000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:39614600-39616800	Enhancers	Fetal Heart	heart
41	chr2:39614600-39617800	Enhancers	Rectal Smooth Muscle	rectum
42	chr2:39614600-39617800	Enhancers	Skeletal Muscle Female	skeletal muscle
43	chr2:39614600-39618000	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr2:39614800-39617400	Weak transcription	Ovary	ovary
45	chr2:39614800-39618800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr2:39614800-39620800	Weak transcription	Right Ventricle	heart
47	chr2:39614800-39621600	Weak transcription	Pancreas	Pancrea
48	chr2:39615200-39619600	Weak transcription	Liver	Liver
49	chr2:39615600-39617400	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr2:39615600-39619000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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