Variant report

Variant	rs17534053
Chromosome Location	chr2:128520262-128520263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:128514646..128516225-chr2:128518378..128520380,2	K562	blood:
2	chr2:128519576..128522158-chr2:128528334..128530118,2	MCF-7	breast:
3	chr2:128458117..128461051-chr2:128519304..128521495,3	MCF-7	breast:
4	chr2:128458705..128461954-chr2:128518715..128522219,4	K562	blood:

Variant related genes	Relation type
ENSG00000173349	Chromatin interaction

Extended variants
information (count: 43 )
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[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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];0.81[EUR][1000 genomes]
rs11692524	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11693223	0.85[AFR][1000 genomes]
rs11693759	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs13397060	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs13421835	0.81[ASN][1000 genomes]
rs13423029	0.81[ASN][1000 genomes]
rs17418125	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17534123	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599575	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]
rs17600177	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3771291	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56954978	1.00[ASN][1000 genomes]
rs57410763	0.86[ASN][1000 genomes]
rs57498556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57913162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57986825	0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58080260	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59009188	0.86[ASN][1000 genomes]
rs59090605	1.00[ASN][1000 genomes]
rs59727076	0.86[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59918187	0.81[ASN][1000 genomes]
rs60087786	1.00[ASN][1000 genomes]
rs61187878	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61730415	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6714620	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[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];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7585200	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591477	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7605158	1.00[JPT][hapmap];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	esv1796560	chr2:128495645-128521448	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17534053	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	chr2:128479400-128560400	Weak transcription	Esophagus	oesophagus
2	chr2:128480200-128521400	Weak transcription	Spleen	Spleen
3	chr2:128492200-128522200	Weak transcription	Aorta	Aorta
4	chr2:128493000-128526800	Weak transcription	Psoas Muscle	Psoas
5	chr2:128493000-128528000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:128496600-128520600	Weak transcription	Brain Germinal Matrix	brain
7	chr2:128498200-128562800	Weak transcription	Pancreas	Pancrea
8	chr2:128498400-128533800	Weak transcription	Right Ventricle	heart
9	chr2:128501400-128527400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:128503000-128521200	Weak transcription	NHLF	lung
11	chr2:128504400-128521800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:128507600-128542800	Weak transcription	Stomach Mucosa	stomach
13	chr2:128508000-128521800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:128508800-128524200	Weak transcription	Fetal Intestine Small	intestine
15	chr2:128509000-128529200	Strong transcription	HUES64 Cell Line	embryonic stem cell
16	chr2:128510800-128529400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:128511000-128529200	Strong transcription	Dnd41	blood
18	chr2:128511800-128529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:128512800-128528200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr2:128513000-128529400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr2:128514400-128529200	Strong transcription	Fetal Thymus	thymus
22	chr2:128514800-128526200	Strong transcription	HSMM	muscle
23	chr2:128514800-128528800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr2:128515000-128526200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr2:128515000-128529000	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr2:128515000-128529200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:128515000-128529200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr2:128515400-128521200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:128515400-128525800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr2:128515400-128528800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr2:128515600-128523200	Strong transcription	A549	lung
32	chr2:128515600-128527000	Strong transcription	Primary B cells from peripheral blood	blood
33	chr2:128515600-128529000	Strong transcription	Primary T cells from cord blood	blood
34	chr2:128515600-128529600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr2:128515800-128526000	Strong transcription	Primary neutrophils fromperipheralblood	blood
36	chr2:128515800-128527800	Strong transcription	NHDF-Ad	bronchial
37	chr2:128515800-128529200	Strong transcription	K562	blood
38	chr2:128516000-128528200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr2:128516200-128528800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr2:128516400-128529000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr2:128516400-128529200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:128516800-128523400	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr2:128517000-128523000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr2:128517400-128528000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr2:128517400-128528400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr2:128517400-128529000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr2:128517400-128529200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr2:128517600-128526000	Strong transcription	Primary hematopoietic stem cells	blood
49	chr2:128517800-128522800	Strong transcription	Placenta Amnion	Placenta Amnion
50	chr2:128517800-128523200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links