Variant report

Variant	rs10174055
Chromosome Location	chr2:172858214-172858215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172856619..172859628-chr2:172864292..172866200,3	MCF-7	breast:
2	chr2:172822392..172824511-chr2:172856207..172858806,2	K562	blood:
3	chr2:172842087..172844341-chr2:172857534..172860058,2	K562	blood:
4	chr2:172857904..172859439-chr2:172876035..172878668,2	K562	blood:
5	chr2:172854755..172858699-chr2:172956896..172962268,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115840	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 19 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10165126	0.88[CEU][hapmap];0.85[MEX][hapmap];0.92[TSI][hapmap]
rs10166548	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10201430	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10202823	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10930502	0.87[CEU][hapmap]
rs12692974	0.87[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs12692978	0.83[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.84[MKK][hapmap]
rs13004237	0.83[AMR][1000 genomes]
rs13017585	0.84[ASW][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap]
rs13030911	0.89[AMR][1000 genomes]
rs2165934	0.83[AMR][1000 genomes]
rs35256122	0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs3770445	0.83[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs3770451	0.87[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs3770452	0.87[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.80[MKK][hapmap]
rs4668414	0.92[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.88[MKK][hapmap]
rs6433319	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6715929	0.96[CEU][hapmap];0.92[TSI][hapmap]
rs6724337	0.87[CEU][hapmap];0.82[CHB][hapmap];0.85[CHD][hapmap];0.88[GIH][hapmap];0.81[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap]
rs6725388	0.92[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs6727017	0.96[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.80[YRI][hapmap];0.82[AMR][1000 genomes]
rs6731562	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs6750058	0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6752812	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.85[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6754817	0.92[ASW][hapmap];0.87[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6759575	0.87[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs7563971	0.85[AMR][1000 genomes]
rs7564089	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7573003	0.87[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]
rs7581072	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7586207	0.87[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap]
rs7602037	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs908670	0.83[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap]
rs908671	0.83[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:19)

SNP	Gene	Cis/trans	Tissue	Source
rs10174055	SLC25A12	cis	cerebellum	SCAN
rs10174055	AC068039.4	cis	Esophagus Muscularis	GTEx
rs10174055	SLC25A12	cis	parietal	SCAN
rs10174055	AC068039.4	cis	lung	GTEx
rs10174055	AC068039.4	cis	Stomach	GTEx
rs10174055	PDK1	cis	cerebellum	SCAN
rs10174055	AC068039.4	cis	Thyroid	GTEx
rs10174055	MYO3B	cis	cerebellum	SCAN
rs10174055	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs10174055	AC068039.4	cis	Esophagus Mucosa	GTEx
rs10174055	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs10174055	AC068039.4	cis	Nerve Tibial	GTEx
rs10174055	AC068039.4	cis	Whole Blood	GTEx
rs10174055	DYNC1I2	cis	lymphoblastoid	seeQTL
rs10174055	AC068039.4	cis	Muscle Skeletal	GTEx
rs10174055	MAP1D	cis	parietal	SCAN
rs10174055	AC068039.4	cis	Heart Left Ventricle	GTEx
rs10174055	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs10174055	DYNC1I2	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172813000-172859200	Weak transcription	Fetal Brain Male	brain
3	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
4	chr2:172847400-172864000	Weak transcription	HSMM	muscle
5	chr2:172848000-172863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr2:172849600-172863800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr2:172850400-172860600	Weak transcription	Primary hematopoietic stem cells	blood
8	chr2:172856600-172863200	Weak transcription	K562	blood
9	chr2:172857400-172858800	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr2:172857600-172858400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:172858000-172858600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:172858000-172859600	Weak transcription	Ovary	ovary
13	chr2:172858000-172860400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:172858200-172860000	Enhancers	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links