Variant report

Variant	rs12942179
Chromosome Location	chr17:19999781-19999782
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10083830	0.90[AMR][1000 genomes]
rs10083840	0.92[AMR][1000 genomes]
rs11204422	1.00[JPT][hapmap];0.91[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11654025	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs11867585	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11869931	1.00[ASN][1000 genomes]
rs11870381	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs11870673	0.85[ASN][1000 genomes]
rs12451216	0.92[ASN][1000 genomes]
rs12451841	0.80[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12453332	0.97[ASN][1000 genomes]
rs12947713	0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs12949710	1.00[ASN][1000 genomes]
rs1468953	1.00[ASN][1000 genomes]
rs1638526	0.81[JPT][hapmap]
rs17685923	1.00[ASN][1000 genomes]
rs17686798	0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs17759083	0.92[AMR][1000 genomes]
rs17759959	0.83[JPT][hapmap];0.90[ASN][1000 genomes]
rs2034110	0.90[JPT][hapmap]
rs28424266	0.81[JPT][hapmap]
rs34370440	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34756775	1.00[ASN][1000 genomes]
rs35003563	0.88[CEU][hapmap]
rs35041742	0.85[ASN][1000 genomes]
rs35124809	1.00[ASN][1000 genomes]
rs35156798	0.97[ASN][1000 genomes]
rs35191778	1.00[ASN][1000 genomes]
rs35244101	1.00[ASN][1000 genomes]
rs35493088	1.00[ASN][1000 genomes]
rs35770292	0.97[ASN][1000 genomes]
rs36051592	0.87[ASN][1000 genomes]
rs4141185	0.81[JPT][hapmap]
rs4341795	1.00[ASN][1000 genomes]
rs4346259	1.00[ASN][1000 genomes]
rs4350625	1.00[ASN][1000 genomes]
rs4471741	1.00[ASN][1000 genomes]
rs4570919	1.00[JPT][hapmap]
rs4924803	0.88[CEU][hapmap]
rs4924808	0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs4925072	0.88[CEU][hapmap]
rs4925075	0.90[JPT][hapmap];1.00[ASN][1000 genomes]
rs4925076	1.00[ASN][1000 genomes]
rs4925077	0.88[CEU][hapmap]
rs4925078	1.00[ASN][1000 genomes]
rs4925081	0.88[CEU][hapmap]
rs4925082	0.80[CEU][hapmap];0.90[JPT][hapmap];0.81[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4925088	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs57146223	0.80[ASN][1000 genomes]
rs62067488	1.00[ASN][1000 genomes]
rs6587207	0.83[JPT][hapmap]
rs7207459	0.83[JPT][hapmap]
rs7207625	0.88[CEU][hapmap]
rs7208025	0.88[CEU][hapmap]
rs7208365	0.88[CEU][hapmap]
rs7209653	0.81[JPT][hapmap]
rs7215803	0.80[CEU][hapmap];0.90[JPT][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7224875	0.90[JPT][hapmap]
rs7503407	1.00[ASN][1000 genomes]
rs8066705	0.88[ASN][1000 genomes]
rs8068484	0.83[JPT][hapmap];0.98[ASN][1000 genomes]
rs8074791	0.88[ASN][1000 genomes]
rs8075343	0.83[JPT][hapmap];1.00[ASN][1000 genomes]
rs8080190	0.90[JPT][hapmap]
rs8081817	1.00[ASN][1000 genomes]
rs888423	0.88[CEU][hapmap]
rs888424	0.80[CEU][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs972966	0.88[ASN][1000 genomes]
rs9897653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9901125	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9901294	0.81[JPT][hapmap]
rs9915039	0.83[JPT][hapmap]
rs9944451	1.00[JPT][hapmap];0.95[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062853	chr17:19547912-20206601	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	nsv907868	chr17:19768924-20217122	Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv1060337	chr17:19828636-20204872	Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv543257	chr17:19828636-20204872	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv907870	chr17:19871922-20001612	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv907871	chr17:19927699-20088492	Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv482438	chr17:19934376-20089005	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv833395	chr17:19969959-20124084	Genic enhancers Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:19978800-20000000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr17:19993400-20006400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr17:19993600-20000000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr17:19993600-20003600	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr17:19993800-20000600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr17:19993800-20001600	Weak transcription	Lung	lung
7	chr17:19993800-20006400	Weak transcription	Esophagus	oesophagus
8	chr17:19993800-20008800	Weak transcription	GM12878-XiMat	blood
9	chr17:19995000-20000000	Weak transcription	Right Ventricle	heart
10	chr17:19995000-20001200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr17:19996600-20000800	Weak transcription	Aorta	Aorta
12	chr17:19998200-20000000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr17:19998200-20000000	Enhancers	Brain Substantia Nigra	brain
14	chr17:19998600-20000400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr17:19998800-20000600	Enhancers	Ovary	ovary
16	chr17:19999000-19999800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr17:19999000-19999800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr17:19999000-20000200	Enhancers	Adipose Nuclei	Adipose
19	chr17:19999000-20002400	Weak transcription	Gastric	stomach
20	chr17:19999000-20006000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr17:19999000-20032800	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr17:19999200-20000000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr17:19999200-20000000	Weak transcription	Right Atrium	heart
24	chr17:19999200-20000200	Enhancers	Brain Cingulate Gyrus	brain
25	chr17:19999200-20000200	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr17:19999200-20000400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr17:19999200-20001400	Weak transcription	Spleen	Spleen
28	chr17:19999200-20001800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr17:19999200-20002000	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr17:19999200-20002600	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr17:19999200-20005000	Weak transcription	H9 Cell Line	embryonic stem cell
32	chr17:19999200-20008800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
33	chr17:19999400-19999800	Enhancers	Brain Hippocampus Middle	brain
34	chr17:19999400-20000000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:19999400-20000400	Enhancers	Brain Anterior Caudate	brain
36	chr17:19999400-20000400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr17:19999400-20004400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr17:19999400-20005000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr17:19999400-20005600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr17:19999400-20011800	Weak transcription	A549	lung
41	chr17:19999600-20000000	Weak transcription	Fetal Muscle Leg	muscle
42	chr17:19999600-20001400	Weak transcription	Brain Angular Gyrus	brain
43	chr17:19999600-20002600	Strong transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links