Variant report

Variant	rs17599575
Chromosome Location	chr2:128480973-128480974
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128479508..128482140-chr2:128488342..128490473,2	K562	blood:
2	chr2:128474798..128481171-chr2:128482515..128488388,6	MCF-7	breast:
3	chr2:128480478..128486458-chr2:128490383..128494380,6	MCF-7	breast:
4	chr2:128460642..128462696-chr2:128480272..128482595,2	MCF-7	breast:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10171898	1.00[ASN][1000 genomes]
rs10210695	1.00[ASN][1000 genomes]
rs11557685	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11674513	1.00[ASN][1000 genomes]
rs11678032	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11682274	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11692524	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs11693223	0.82[AFR][1000 genomes]
rs11693759	1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13397060	1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[ASN][1000 genomes]
rs13421835	0.81[ASN][1000 genomes]
rs13423029	0.81[ASN][1000 genomes]
rs17418125	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534053	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534123	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600177	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771291	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56954978	1.00[ASN][1000 genomes]
rs57410763	0.86[ASN][1000 genomes]
rs57498556	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57913162	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57986825	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58080260	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59009188	0.86[ASN][1000 genomes]
rs59090605	1.00[ASN][1000 genomes]
rs59727076	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59918187	0.81[ASN][1000 genomes]
rs60087786	1.00[ASN][1000 genomes]
rs61187878	1.00[ASN][1000 genomes]
rs61730415	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714620	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6734925	1.00[ASN][1000 genomes]
rs6756507	1.00[ASN][1000 genomes]
rs72963794	1.00[ASN][1000 genomes]
rs7560482	0.81[ASN][1000 genomes]
rs7574303	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs7575961	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585200	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591477	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605158	1.00[JPT][hapmap];1.00[ASN][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	nsv875015	chr2:128305196-128495645	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	esv3368061	chr2:128375044-128672849	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv428726	chr2:128387756-128539894	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv875030	chr2:128399414-128495645	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	36 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17599575	WDR33	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:128460400-128483000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr2:128460400-128520000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:128461200-128482800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:128461200-128485600	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr2:128463400-128484800	Strong transcription	Thymus	Thymus
6	chr2:128466400-128481800	Strong transcription	Fetal Muscle Trunk	muscle
7	chr2:128466400-128490200	Weak transcription	Right Atrium	heart
8	chr2:128469600-128484400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
9	chr2:128469800-128482600	Strong transcription	Primary T helper cells fromperipheralblood	blood
10	chr2:128470000-128482800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr2:128470000-128483000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:128470000-128484600	Strong transcription	HUES48 Cell Line	embryonic stem cell
13	chr2:128471000-128482600	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:128471000-128482600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr2:128471200-128482600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:128471200-128482800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:128471200-128482800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr2:128471200-128484400	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr2:128471600-128482800	Strong transcription	Primary B cells from cord blood	blood
20	chr2:128471800-128482800	Strong transcription	GM12878-XiMat	blood
21	chr2:128472800-128483000	Strong transcription	Fetal Thymus	thymus
22	chr2:128472800-128483000	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr2:128473000-128482400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr2:128473000-128482600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr2:128473000-128484000	Strong transcription	Dnd41	blood
26	chr2:128473200-128482400	Strong transcription	Primary T helper cells PMA-I stimulated	--
27	chr2:128473200-128482800	Strong transcription	Primary neutrophils fromperipheralblood	blood
28	chr2:128473600-128482600	Strong transcription	Primary hematopoietic stem cells	blood
29	chr2:128473600-128482800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr2:128473800-128481000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr2:128473800-128481200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr2:128473800-128482600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:128473800-128484600	Strong transcription	HUES64 Cell Line	embryonic stem cell
34	chr2:128474000-128481000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr2:128474200-128481000	Strong transcription	Primary B cells from peripheral blood	blood
36	chr2:128474200-128482200	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr2:128474200-128484000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
38	chr2:128475400-128485600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr2:128475600-128482600	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr2:128475800-128481200	Strong transcription	Colon Smooth Muscle	Colon
41	chr2:128475800-128481600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr2:128475800-128481600	Strong transcription	Lung	lung
43	chr2:128475800-128482600	Strong transcription	Duodenum Mucosa	Duodenum
44	chr2:128475800-128482600	Strong transcription	Fetal Intestine Large	intestine
45	chr2:128475800-128482800	Strong transcription	Liver	Liver
46	chr2:128475800-128482800	Strong transcription	Placenta	Placenta
47	chr2:128476000-128481000	Strong transcription	HUVEC	blood vessel
48	chr2:128476000-128482800	Strong transcription	H9 Cell Line	embryonic stem cell
49	chr2:128476000-128483400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr2:128476200-128482200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links