Variant report

Variant	rs17730901
Chromosome Location	chr20:16250822-16250823
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:16243563..16246157-chr20:16249684..16251577,2	K562	blood:
2	chr20:16243563..16246157-chr20:16249683..16251577,3	K562	blood:
3	chr20:16250737..16252251-chr20:16257210..16259661,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10485549	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10485550	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11907241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11908227	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11908242	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11908381	0.87[AFR][1000 genomes]
rs16997595	1.00[JPT][hapmap]
rs17730831	1.00[ASN][1000 genomes]
rs17731020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2144896	0.82[CHB][hapmap]
rs3848791	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3848792	1.00[ASN][1000 genomes]
rs3848793	1.00[ASN][1000 genomes]
rs4052895	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41276366	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4287828	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4416282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814466	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4814467	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57988134	1.00[ASN][1000 genomes]
rs6105560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6105561	1.00[ASN][1000 genomes]
rs6105562	1.00[ASN][1000 genomes]
rs6105564	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];0.83[TSI][hapmap]
rs6110998	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6110999	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6111001	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111005	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111007	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111008	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6111012	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6111025	0.90[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs718610	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs878582	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs878583	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833930	chr20:16134347-16302763	Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17730901	LOC100130264	cis	cerebellum	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:16242400-16275000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr20:16244800-16253400	Weak transcription	Ovary	ovary
3	chr20:16246600-16253200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr20:16247400-16253600	Weak transcription	Gastric	stomach
5	chr20:16247600-16253200	Weak transcription	Duodenum Mucosa	Duodenum
6	chr20:16247600-16290800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr20:16248000-16254400	Weak transcription	Fetal Muscle Leg	muscle
8	chr20:16248200-16253400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr20:16248200-16253600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr20:16248200-16255400	Weak transcription	Placenta	Placenta
11	chr20:16248400-16259400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr20:16248400-16260800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr20:16248400-16261000	Weak transcription	Left Ventricle	heart
14	chr20:16248400-16263200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr20:16248400-16263800	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr20:16248600-16253200	Weak transcription	NHEK	skin
17	chr20:16248600-16253400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr20:16248600-16253600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr20:16248600-16253600	Weak transcription	Fetal Stomach	stomach
20	chr20:16248600-16253600	Weak transcription	Pancreas	Pancrea
21	chr20:16248600-16253600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr20:16248600-16291400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr20:16248800-16251800	Weak transcription	Adipose Nuclei	Adipose
24	chr20:16248800-16253600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr20:16248800-16253600	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr20:16248800-16253600	Weak transcription	Lung	lung
27	chr20:16248800-16253600	Weak transcription	Spleen	Spleen
28	chr20:16248800-16256600	Weak transcription	Primary B cells from peripheral blood	blood
29	chr20:16248800-16267000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr20:16248800-16272600	Weak transcription	Primary T cells from cord blood	blood
31	chr20:16249000-16251800	Weak transcription	Fetal Intestine Small	intestine
32	chr20:16249000-16253800	Weak transcription	Aorta	Aorta
33	chr20:16249000-16272800	Weak transcription	Right Ventricle	heart
34	chr20:16249200-16251800	Weak transcription	Rectal Mucosa Donor 31	rectum
35	chr20:16249200-16277400	Weak transcription	Brain Substantia Nigra	brain
36	chr20:16249400-16253400	Weak transcription	Esophagus	oesophagus
37	chr20:16249400-16264000	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr20:16250000-16252000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr20:16250000-16266800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr20:16250400-16255600	Enhancers	Fetal Brain Male	brain
41	chr20:16250600-16251400	Weak transcription	Fetal Brain Female	brain
42	chr20:16250600-16253000	Weak transcription	Primary hematopoietic stem cells	blood
43	chr20:16250600-16260600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr20:16250800-16251200	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr20:16250800-16263400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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