Variant report

Variant	rs17406229
Chromosome Location	chr2:187549354-187549355
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:187535669..187538120-chr2:187548739..187551384,2	K562	blood:
2	chr2:187547487..187550393-chr2:187552355..187554929,3	K562	blood:

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

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10165992	0.92[CEU][hapmap];0.88[CHB][hapmap]
rs1072901	0.88[CHB][hapmap];0.80[ASN][1000 genomes]
rs10755000	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10931253	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12475476	0.94[CHB][hapmap];0.82[ASN][1000 genomes]
rs12618322	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12620821	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.88[MEX][hapmap];0.81[MKK][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13020260	0.88[CHB][hapmap]
rs13028008	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1448427	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs17406346	0.88[CHB][hapmap]
rs2121975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2121976	1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2290083	0.83[ASN][1000 genomes]
rs2595395	0.92[CEU][hapmap];0.88[CHB][hapmap];0.86[TSI][hapmap]
rs2682868	0.86[EUR][1000 genomes]
rs2682873	1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[EUR][1000 genomes]
rs3213964	0.83[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.88[MEX][hapmap];0.84[MKK][hapmap];0.91[ASN][1000 genomes]
rs34056045	0.81[ASN][1000 genomes]
rs34840521	0.91[ASN][1000 genomes]
rs35348196	0.91[ASN][1000 genomes]
rs3768785	0.88[CHB][hapmap]
rs3816375	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs41265951	0.81[ASN][1000 genomes]
rs4667108	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.88[ASN][1000 genomes]
rs4667112	0.82[ASN][1000 genomes]
rs4667113	0.81[ASN][1000 genomes]
rs55961288	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56222785	0.88[ASN][1000 genomes]
rs6705757	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.92[JPT][hapmap];0.88[LWK][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs718259	0.88[CHB][hapmap]
rs7585442	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs7585471	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.87[ASN][1000 genomes]
rs930657	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9789704	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[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	esv2757844	chr2:187332780-187580547	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv2759107	chr2:187332780-187580547	Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17406229	DNAJC10	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:187536400-187550000	Weak transcription	Gastric	stomach
2	chr2:187538200-187552800	Weak transcription	Brain Substantia Nigra	brain
3	chr2:187539200-187557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr2:187541600-187550800	Weak transcription	Lung	lung
5	chr2:187541800-187550400	Weak transcription	Fetal Stomach	stomach
6	chr2:187541800-187552800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr2:187541800-187558400	Weak transcription	Left Ventricle	heart
8	chr2:187542000-187549600	Weak transcription	Right Ventricle	heart
9	chr2:187542000-187550200	Weak transcription	Aorta	Aorta
10	chr2:187542000-187550200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr2:187542000-187555400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:187543400-187549600	Weak transcription	Fetal Intestine Large	intestine
13	chr2:187543400-187558200	Weak transcription	NHDF-Ad	bronchial
14	chr2:187543600-187558200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:187543800-187549600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr2:187546000-187552000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr2:187546200-187558200	Weak transcription	Placenta	Placenta
18	chr2:187546800-187549400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr2:187546800-187549600	Weak transcription	NH-A	brain
20	chr2:187546800-187558000	Weak transcription	A549	lung
21	chr2:187547200-187549800	Weak transcription	HSMMtube	muscle
22	chr2:187547200-187549800	Weak transcription	HUVEC	blood vessel
23	chr2:187547200-187550000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links