Variant report

Variant	rs2417190
Chromosome Location	chr12:12651039-12651040
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	chr12:12645901..12648123-chr12:12648969..12651125,3	MCF-7	breast:
2	chr12:12644427..12647332-chr12:12650507..12652988,2	K562	blood:

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10743988	0.92[ASN][1000 genomes]
rs10772570	0.80[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10845552	0.86[CHB][hapmap]
rs10845559	0.90[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs10845560	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs10845567	0.94[CHB][hapmap];0.80[JPT][hapmap];0.92[ASN][1000 genomes]
rs10845568	0.83[EUR][1000 genomes]
rs10845572	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11054937	0.93[ASN][1000 genomes]
rs11054940	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054941	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][1000 genomes]
rs11054942	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11054947	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11610879	0.83[EUR][1000 genomes]
rs11613385	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12422540	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs1558822	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2111271	0.91[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs3815591	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4255620	0.93[ASN][1000 genomes]
rs4763832	0.87[ASN][1000 genomes]
rs4763833	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7137455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294378	0.84[ASN][1000 genomes]
rs7295305	1.00[CHB][hapmap];0.90[JPT][hapmap];0.90[YRI][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7295427	0.90[ASN][1000 genomes]
rs7308097	0.93[YRI][hapmap];0.84[AFR][1000 genomes]
rs7310652	0.93[ASN][1000 genomes]
rs7972902	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs933575	0.95[CHB][hapmap];0.81[JPT][hapmap];0.92[ASN][1000 genomes]
rs962928	1.00[CHB][hapmap];0.81[JPT][hapmap];0.93[ASN][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	esv2758295	chr12:12620654-12783124	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
2	esv2759880	chr12:12620654-12783124	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12610800-12658000	Weak transcription	NHDF-Ad	bronchial
2	chr12:12622600-12653800	Weak transcription	Fetal Heart	heart
3	chr12:12626800-12653600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:12628800-12655800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr12:12630600-12661200	Weak transcription	NHEK	skin
6	chr12:12630800-12655800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:12630800-12658200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:12630800-12658400	Weak transcription	Rectal Smooth Muscle	rectum
9	chr12:12630800-12659600	Weak transcription	Esophagus	oesophagus
10	chr12:12630800-12681000	Weak transcription	Colonic Mucosa	Colon
11	chr12:12632800-12658200	Weak transcription	Ovary	ovary
12	chr12:12633000-12658600	Weak transcription	Fetal Kidney	kidney
13	chr12:12634400-12685200	Weak transcription	Hela-S3	cervix
14	chr12:12634800-12658800	Weak transcription	HSMMtube	muscle
15	chr12:12636000-12653400	Weak transcription	Right Ventricle	heart
16	chr12:12636200-12655800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:12636800-12656800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:12637200-12651600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr12:12639400-12652800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr12:12639400-12679600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr12:12639600-12655800	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr12:12639600-12659000	Weak transcription	Stomach Smooth Muscle	stomach
23	chr12:12640000-12652800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr12:12640000-12656600	Weak transcription	Colon Smooth Muscle	Colon
25	chr12:12640000-12658000	Weak transcription	NHLF	lung
26	chr12:12640000-12658200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:12640000-12658200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr12:12640000-12658200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:12640200-12652200	Weak transcription	Placenta	Placenta
30	chr12:12640200-12652800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr12:12640200-12656600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:12640400-12659200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:12641200-12658200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:12641400-12652600	Weak transcription	A549	lung
35	chr12:12641600-12658800	Weak transcription	HUVEC	blood vessel
36	chr12:12641600-12663600	Weak transcription	Lung	lung
37	chr12:12641600-12686200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr12:12641800-12654000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:12642200-12652400	Weak transcription	Fetal Thymus	thymus
40	chr12:12642400-12653200	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr12:12643200-12652800	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr12:12645400-12655800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr12:12646200-12652600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:12646200-12652800	Enhancers	Brain Hippocampus Middle	brain
45	chr12:12646200-12658200	Weak transcription	Aorta	Aorta
46	chr12:12646400-12654200	Weak transcription	Primary T helper cells fromperipheralblood	blood
47	chr12:12646400-12655800	Weak transcription	Small Intestine	intestine
48	chr12:12646400-12658000	Weak transcription	K562	blood
49	chr12:12646600-12652600	Weak transcription	Primary T cells from cord blood	blood
50	chr12:12646600-12653400	Weak transcription	Fetal Stomach	stomach

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