Variant report

Variant	rs12490970
Chromosome Location	chr3:194881716-194881717
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194836997..194839918-chr3:194880679..194883112,2	K562	blood:
2	chr15:75660465..75661085-chr3:194881702..194882202,2	MCF-7	breast:
3	chr3:194872665..194876358-chr3:194881191..194883259,3	K562	blood:
4	chr3:194881175..194883958-chr3:194892435..194894199,2	K562	blood:
5	chr3:194870262..194872274-chr3:194880520..194882642,2	K562	blood:
6	chr3:194879677..194882151-chr3:194884432..194886543,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140400	Chromatin interaction
ENSG00000173950	Chromatin interaction
ENSG00000260274	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12496868	1.00[AFR][1000 genomes]
rs12631534	0.96[ASN][1000 genomes]
rs12634183	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2410805	1.00[AFR][1000 genomes]
rs6794662	0.94[ASN][1000 genomes]
rs7628353	0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9830280	0.81[ASN][1000 genomes]
rs9841564	0.81[ASN][1000 genomes]
rs9883144	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	nsv1012592	chr3:194814446-194931562	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
7	nsv536875	chr3:194814446-194931562	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1001492	chr3:194814990-194935397	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
9	nsv461126	chr3:194817484-194961888	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv592981	chr3:194817484-194961888	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
11	nsv878137	chr3:194822098-194900432	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
12	nsv461127	chr3:194833940-194934634	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
13	nsv592982	chr3:194833940-194934634	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1014826	chr3:194834615-195631793	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
15	nsv536876	chr3:194834615-195631793	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	73 gene(s)	inside rSNPs	diseases
16	nsv533904	chr3:194868329-195438728	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	65 gene(s)	inside rSNPs	diseases
17	nsv1009120	chr3:194874494-194974672	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
18	nsv1010168	chr3:194874494-195135790	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
19	nsv536877	chr3:194874494-195135790	Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
20	nsv997956	chr3:194879534-195087539	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS 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
21	nsv536878	chr3:194879534-195087539	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer 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

No data

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194862400-194897800	Weak transcription	Dnd41	blood
2	chr3:194868800-194885400	Enhancers	Fetal Muscle Leg	muscle
3	chr3:194871400-194887400	Enhancers	Primary hematopoietic stem cells	blood
4	chr3:194871800-194882800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:194872000-194882800	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr3:194872000-194883000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr3:194872000-194883000	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr3:194873000-194884400	Enhancers	Primary B cells from peripheral blood	blood
9	chr3:194873000-194884600	Enhancers	Fetal Thymus	thymus
10	chr3:194874000-194889800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:194876600-194893000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:194876800-194893800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr3:194877200-194884200	Weak transcription	Gastric	stomach
14	chr3:194877200-194891200	Weak transcription	Psoas Muscle	Psoas
15	chr3:194877400-194883000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr3:194877400-194888600	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr3:194877400-194888800	Weak transcription	Brain Germinal Matrix	brain
18	chr3:194877800-194881800	Enhancers	Fetal Intestine Small	intestine
19	chr3:194877800-194882800	Weak transcription	Brain Angular Gyrus	brain
20	chr3:194877800-194883000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr3:194878000-194882200	Enhancers	Fetal Intestine Large	intestine
22	chr3:194878200-194882200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:194878200-194882400	Enhancers	Fetal Heart	heart
24	chr3:194878200-194885200	Enhancers	Fetal Stomach	stomach
25	chr3:194878600-194882600	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:194878600-194883000	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:194879000-194883000	Weak transcription	Thymus	Thymus
28	chr3:194879600-194883400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr3:194880000-194881800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:194880000-194881800	Enhancers	Fetal Lung	lung
31	chr3:194880000-194881800	Enhancers	Right Ventricle	heart
32	chr3:194880000-194881800	Enhancers	Small Intestine	intestine
33	chr3:194880000-194882200	Enhancers	Adipose Nuclei	Adipose
34	chr3:194880000-194883000	Enhancers	Placenta	Placenta
35	chr3:194880000-194883200	Enhancers	Left Ventricle	heart
36	chr3:194880000-194883400	Enhancers	Lung	lung
37	chr3:194880000-194883600	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr3:194880000-194887400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr3:194880200-194881800	Enhancers	HSMMtube	muscle
40	chr3:194880200-194882000	Enhancers	Duodenum Mucosa	Duodenum
41	chr3:194880200-194882200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:194880200-194883400	Enhancers	Fetal Muscle Trunk	muscle
43	chr3:194880200-194883400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:194880200-194885000	Enhancers	K562	blood
45	chr3:194880200-194886400	Enhancers	Spleen	Spleen
46	chr3:194880400-194881800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:194880800-194881800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr3:194880800-194882800	Enhancers	GM12878-XiMat	blood
49	chr3:194880800-194883600	Enhancers	Primary B cells from cord blood	blood
50	chr3:194880800-194887200	Enhancers	Primary monocytes fromperipheralblood	blood

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