Variant report

Variant	rs62257009
Chromosome Location	chr3:53374417-53374418
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:53373719..53376064-chr3:53376778..53378854,2	K562	blood:
2	chr3:53372908..53377239-chr3:53377354..53382827,7	K562	blood:

Variant related genes	Relation type
ENSG00000162290	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10433617	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10433618	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1108506	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17030934	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17234771	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17235667	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41275543	0.82[AMR][1000 genomes]
rs56654807	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs59145995	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62252819	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62255989	0.85[AMR][1000 genomes]
rs62255993	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62255994	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62255999	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62256000	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62256003	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62256009	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256043	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256049	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256050	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256053	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256965	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256966	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256968	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256969	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257004	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257007	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257011	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257013	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257024	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6780100	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6805246	0.89[ASN][1000 genomes]
rs73080266	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73082274	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622159	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9830594	0.90[EUR][1000 genomes]
rs9830895	0.92[EUR][1000 genomes]
rs9846315	0.94[EUR][1000 genomes]
rs9850440	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876801	chr3:53325905-53467506	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
2	nsv876802	chr3:53325905-53470863	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53338200-53380200	Weak transcription	Fetal Brain Male	brain
2	chr3:53346200-53378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr3:53346600-53380600	Weak transcription	Spleen	Spleen
4	chr3:53352800-53380600	Weak transcription	Esophagus	oesophagus
5	chr3:53353000-53374600	Weak transcription	Fetal Brain Female	brain
6	chr3:53353000-53380600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:53353400-53377000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr3:53358200-53378800	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:53358400-53380600	Weak transcription	Lung	lung
10	chr3:53358800-53376200	Weak transcription	K562	blood
11	chr3:53360400-53376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:53360600-53380400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr3:53360800-53375800	Weak transcription	Aorta	Aorta
14	chr3:53360800-53380600	Weak transcription	Gastric	stomach
15	chr3:53361400-53380200	Weak transcription	Colonic Mucosa	Colon
16	chr3:53361600-53379000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr3:53362600-53376200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr3:53362600-53376400	Weak transcription	Stomach Mucosa	stomach
19	chr3:53362800-53378200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
20	chr3:53362800-53380400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:53363200-53375200	Weak transcription	Ovary	ovary
22	chr3:53363200-53376600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr3:53363200-53378400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:53363200-53380600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr3:53363400-53380400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr3:53363600-53378800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr3:53363800-53379000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr3:53364200-53377800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:53364400-53378600	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr3:53364600-53376600	Weak transcription	Right Ventricle	heart
31	chr3:53365000-53378800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:53365200-53376400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:53365200-53376400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:53365200-53376600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:53365400-53377600	Strong transcription	Osteobl	bone
36	chr3:53365400-53378200	Strong transcription	Fetal Lung	lung
37	chr3:53365400-53378600	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr3:53365600-53377800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr3:53365600-53378800	Strong transcription	Placenta	Placenta
40	chr3:53365600-53379200	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr3:53366200-53376600	Weak transcription	Brain Anterior Caudate	brain
42	chr3:53366200-53376800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:53366200-53379800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:53366200-53380200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr3:53367200-53376400	Strong transcription	HUVEC	blood vessel
46	chr3:53367200-53378800	Strong transcription	Primary B cells from peripheral blood	blood
47	chr3:53367400-53375000	Strong transcription	Primary hematopoietic stem cells	blood
48	chr3:53367400-53376400	Strong transcription	Primary T helper cells PMA-I stimulated	--
49	chr3:53367400-53376400	Strong transcription	Liver	Liver
50	chr3:53367400-53378400	Strong transcription	Primary B cells from cord blood	blood

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