Variant report

Variant	rs10490469
Chromosome Location	chr2:53989984-53989985
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr2:53989899-53990072	MCF10A-Er-Src	breast:	n/a	n/a

Variant related genes	Relation type
CHAC2	TF binding region

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10490466	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10490467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11125516	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11676319	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11676512	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11681941	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11689950	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11692732	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11693306	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17520680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17521418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17578919	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17580080	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs34498147	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs55891349	1.00[ASN][1000 genomes]
rs56273260	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56278932	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58445692	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6715313	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7349309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][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	nsv1003263	chr2:53863287-54055359	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv535720	chr2:53863287-54055359	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv834058	chr2:53900674-54072011	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	nsv1009829	chr2:53980562-54051927	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:53910000-53994000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr2:53910200-53990600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr2:53918400-53994000	Weak transcription	Fetal Heart	heart
4	chr2:53937000-53994400	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr2:53937200-53994200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr2:53937400-53990200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr2:53937400-53994400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr2:53938400-53992400	Weak transcription	K562	blood
9	chr2:53958200-53994400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:53963000-53994000	Weak transcription	A549	lung
11	chr2:53967200-53990200	Weak transcription	Gastric	stomach
12	chr2:53971200-53990200	Weak transcription	Pancreas	Pancrea
13	chr2:53973400-53994400	Weak transcription	Colonic Mucosa	Colon
14	chr2:53975600-53990200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr2:53975800-53994400	Weak transcription	Fetal Kidney	kidney
16	chr2:53978200-53990200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr2:53978800-53994200	Weak transcription	Rectal Smooth Muscle	rectum
18	chr2:53979200-53990200	Weak transcription	HUVEC	blood vessel
19	chr2:53979400-53994000	Weak transcription	Osteobl	bone
20	chr2:53979800-53990200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:53979800-53990200	Weak transcription	Esophagus	oesophagus
22	chr2:53979800-53994200	Weak transcription	Psoas Muscle	Psoas
23	chr2:53979800-53994200	Weak transcription	NHLF	lung
24	chr2:53980000-53990200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr2:53980600-53990400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr2:53981600-53990200	Weak transcription	Aorta	Aorta
27	chr2:53982400-53990200	Weak transcription	NHEK	skin
28	chr2:53982400-53990800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr2:53982400-53991600	Weak transcription	Stomach Mucosa	stomach
30	chr2:53982400-53991800	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr2:53982400-53994400	Weak transcription	NHDF-Ad	bronchial
32	chr2:53982800-53990200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:53982800-53994000	Weak transcription	HMEC	breast
34	chr2:53982800-53994200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:53983000-53994000	Weak transcription	Small Intestine	intestine
36	chr2:53983200-53990400	Weak transcription	Hela-S3	cervix
37	chr2:53983200-53993200	Strong transcription	Primary T cells from cord blood	blood
38	chr2:53984000-53990200	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr2:53984000-53990400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:53984200-53990000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:53984200-53990200	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr2:53984200-53990200	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:53984200-53990200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:53984200-53990200	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr2:53984200-53990200	Weak transcription	Spleen	Spleen
46	chr2:53984200-53990600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr2:53984200-53992800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr2:53984200-53993000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr2:53984200-53994200	Weak transcription	HSMMtube	muscle
50	chr2:53984200-53994400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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