Variant report

Variant	rs62256969
Chromosome Location	chr3:53359150-53359151
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:53358410..53361188-chr3:53381021..53382668,2	K562	blood:
2	chr3:53357519..53359910-chr3:53380664..53382668,2	K562	blood:
3	chr3:53357128..53359838-chr3:53370789..53372378,2	MCF-7	breast:

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];0.93[EUR][1000 genomes]
rs10433618	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1108506	0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11551405	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17030933	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17030934	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17234771	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17235667	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41275543	0.82[AMR][1000 genomes]
rs56654807	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58558806	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59145995	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62252819	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs62255989	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62255993	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62255994	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62255999	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62256000	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62256003	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62256009	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256043	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62256049	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62256050	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62256053	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256962	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256964	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256965	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256966	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62256968	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257004	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257007	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257009	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62257011	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257013	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62257024	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6780100	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6805246	0.89[ASN][1000 genomes]
rs73080266	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080271	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080273	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73080295	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73082274	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7622159	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9830594	0.91[EUR][1000 genomes]
rs9830895	0.93[EUR][1000 genomes]
rs9846315	0.95[EUR][1000 genomes]
rs9850440	0.94[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:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53326600-53364400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:53338000-53374000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:53338200-53380200	Weak transcription	Fetal Brain Male	brain
4	chr3:53338400-53367400	Weak transcription	Small Intestine	intestine
5	chr3:53344000-53364200	Weak transcription	Right Ventricle	heart
6	chr3:53345800-53362600	Weak transcription	NHLF	lung
7	chr3:53346000-53373600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr3:53346200-53365200	Weak transcription	Fetal Kidney	kidney
9	chr3:53346200-53378600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:53346400-53360400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr3:53346400-53360400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:53346400-53360400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:53346400-53360400	Weak transcription	Aorta	Aorta
14	chr3:53346400-53360400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:53346400-53362200	Weak transcription	Stomach Mucosa	stomach
16	chr3:53346400-53362800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:53346400-53365400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:53346400-53367600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr3:53346400-53370000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr3:53346600-53380600	Weak transcription	Spleen	Spleen
21	chr3:53347000-53359200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:53347200-53360400	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr3:53347200-53371400	Weak transcription	HMEC	breast
24	chr3:53347400-53360600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr3:53352000-53362200	Weak transcription	Right Atrium	heart
26	chr3:53352200-53365400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr3:53352800-53380600	Weak transcription	Esophagus	oesophagus
28	chr3:53353000-53360400	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:53353000-53360400	Weak transcription	Thymus	Thymus
30	chr3:53353000-53374600	Weak transcription	Fetal Brain Female	brain
31	chr3:53353000-53380600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr3:53353200-53359800	Weak transcription	Primary T cells from cord blood	blood
33	chr3:53353200-53360400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr3:53353200-53360400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:53353200-53360400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:53353200-53360400	Weak transcription	Colonic Mucosa	Colon
37	chr3:53353200-53365200	Weak transcription	HSMM	muscle
38	chr3:53353200-53365400	Weak transcription	NH-A	brain
39	chr3:53353400-53360400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr3:53353400-53360400	Weak transcription	Fetal Intestine Large	intestine
41	chr3:53353400-53360800	Weak transcription	Brain Germinal Matrix	brain
42	chr3:53353400-53377000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:53353600-53360400	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr3:53353600-53360400	Weak transcription	Brain Hippocampus Middle	brain
45	chr3:53353600-53360400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr3:53353600-53365400	Weak transcription	NHDF-Ad	bronchial
47	chr3:53353800-53359600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr3:53353800-53359800	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:53353800-53360400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:53353800-53360400	Weak transcription	HUVEC	blood vessel

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