Variant report

Variant	rs13407488
Chromosome Location	chr2:36626423-36626424
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:36583520..36585137-chr2:36624819..36626456,2	MCF-7	breast:
2	chr2:36621514..36623196-chr2:36625888..36628234,2	K562	blood:
3	chr2:36624404..36627384-chr2:36629683..36631735,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150938	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10178804	1.00[CHB][hapmap]
rs10186135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10203010	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11124515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11124516	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1159133	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12465282	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12465297	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12477836	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12994926	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13394052	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2689711	1.00[JPT][hapmap]
rs3755214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3770913	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3770924	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs3770932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3770936	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3770946	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs3770947	0.85[CEU][hapmap];1.00[JPT][hapmap]
rs4233914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4670547	1.00[CHB][hapmap]
rs4670548	0.80[AFR][1000 genomes]
rs4670554	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6711707	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6755048	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs711255	1.00[JPT][hapmap]
rs7589917	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs848506	0.87[ASN][1000 genomes]
rs848508	1.00[JPT][hapmap]
rs848513	1.00[JPT][hapmap]
rs848514	1.00[JPT][hapmap]
rs888075	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888076	0.81[CEU][hapmap];1.00[JPT][hapmap]
rs9308991	1.00[CHB][hapmap]
rs9308992	1.00[CHB][hapmap]
rs997602	1.00[CHB][hapmap]

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	nsv833803	chr2:36589065-36745779	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv2756915	chr2:36622906-36657305	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	esv2759041	chr2:36622906-36657305	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	Chromatin interactive region	1 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	chr2:36586200-36626600	Weak transcription	Primary B cells from cord blood	blood
2	chr2:36604400-36640400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr2:36604400-36640600	Weak transcription	Brain Cingulate Gyrus	brain
4	chr2:36611600-36632400	Weak transcription	Esophagus	oesophagus
5	chr2:36611600-36635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:36616800-36631200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr2:36616800-36635000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr2:36617000-36633400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr2:36617200-36630800	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:36617200-36631200	Weak transcription	Fetal Kidney	kidney
11	chr2:36617200-36633800	Weak transcription	Fetal Lung	lung
12	chr2:36617800-36630600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:36617800-36630600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr2:36618600-36643000	Genic enhancers	Osteobl	bone
15	chr2:36620200-36635000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:36620800-36629200	Genic enhancers	Muscle Satellite Cultured Cells	--
17	chr2:36621000-36630600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:36621000-36631400	Weak transcription	Fetal Brain Female	brain
19	chr2:36621000-36635000	Weak transcription	Stomach Smooth Muscle	stomach
20	chr2:36621000-36635200	Weak transcription	Lung	lung
21	chr2:36621200-36628000	Weak transcription	Ovary	ovary
22	chr2:36621200-36629000	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:36621200-36630800	Weak transcription	Spleen	Spleen
24	chr2:36621200-36634800	Weak transcription	Brain Hippocampus Middle	brain
25	chr2:36621200-36634800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr2:36621200-36635000	Weak transcription	Fetal Stomach	stomach
27	chr2:36622600-36628000	Genic enhancers	NHDF-Ad	bronchial
28	chr2:36622600-36630600	Genic enhancers	HUVEC	blood vessel
29	chr2:36622800-36629000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr2:36622800-36629400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr2:36622800-36630600	Weak transcription	Colon Smooth Muscle	Colon
32	chr2:36622800-36631400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr2:36623000-36632200	Weak transcription	Right Atrium	heart
34	chr2:36623400-36629600	Strong transcription	Placenta	Placenta
35	chr2:36623600-36627200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr2:36623600-36630800	Genic enhancers	NHLF	lung
37	chr2:36624000-36626800	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr2:36624000-36627200	Strong transcription	Primary hematopoietic stem cells	blood
39	chr2:36624000-36631400	Enhancers	Psoas Muscle	Psoas
40	chr2:36624200-36629600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
41	chr2:36624200-36635000	Weak transcription	Brain Angular Gyrus	brain
42	chr2:36624400-36626600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:36624400-36626600	Strong transcription	NH-A	brain
44	chr2:36624400-36627000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr2:36624400-36627400	Weak transcription	Aorta	Aorta
46	chr2:36624400-36627600	Weak transcription	Brain Anterior Caudate	brain
47	chr2:36624400-36627800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr2:36624400-36628000	Strong transcription	HMEC	breast
49	chr2:36624400-36628600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr2:36624400-36630800	Weak transcription	Small Intestine	intestine

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