Variant report

Variant	rs227419
Chromosome Location	chr14:70459370-70459371
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:70456335-70461656	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:70458044..70460070-chr14:70460426..70463447,3	MCF-7	breast:

Variant related genes	Relation type
SMOC1	TF binding region
ENSG00000198732	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10134291	0.93[GIH][hapmap]
rs10134965	0.93[GIH][hapmap]
rs11158827	0.97[GIH][hapmap];0.84[TSI][hapmap]
rs12050076	0.82[CHB][hapmap];0.80[CHD][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs12433177	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12885683	0.93[GIH][hapmap]
rs1471243	0.82[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs17107547	0.81[ASN][1000 genomes]
rs17107592	0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs17107610	0.93[GIH][hapmap]
rs182745	0.86[CHD][hapmap]
rs192024	0.81[CHB][hapmap];0.91[CHD][hapmap];0.82[ASN][1000 genomes]
rs227412	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.94[ASN][1000 genomes]
rs227416	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs227417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap]
rs227420	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs227422	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.98[ASN][1000 genomes]
rs227423	0.98[ASN][1000 genomes]
rs227424	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227425	0.95[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.98[ASN][1000 genomes]
rs227426	0.88[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227427	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227437	0.84[CHD][hapmap];0.81[ASN][1000 genomes]
rs227438	0.96[CEU][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227439	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs227444	0.91[JPT][hapmap]
rs56031625	0.89[ASN][1000 genomes]
rs61305	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs67294558	0.81[ASN][1000 genomes]
rs7151788	0.82[CHB][hapmap];0.80[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs8012912	0.97[GIH][hapmap];0.83[MEX][hapmap]

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	nsv456336	chr14:70081956-70574149	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
2	nsv565007	chr14:70081956-70574149	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv832824	chr14:70320639-70511401	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs227419	SMOC1	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:70439800-70477200	Weak transcription	Spleen	Spleen
2	chr14:70450600-70464800	Weak transcription	Fetal Stomach	stomach
3	chr14:70450600-70477200	Weak transcription	Fetal Brain Female	brain
4	chr14:70452800-70460600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr14:70453000-70464800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr14:70453200-70462600	Weak transcription	NHEK	skin
7	chr14:70453600-70462600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr14:70454800-70460800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:70456800-70463800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:70456800-70463800	Weak transcription	Pancreas	Pancrea
11	chr14:70457000-70459400	Weak transcription	Hela-S3	cervix
12	chr14:70457400-70464200	Weak transcription	HepG2	liver
13	chr14:70457800-70459600	Enhancers	Fetal Intestine Small	intestine
14	chr14:70457800-70484800	Weak transcription	Brain Substantia Nigra	brain
15	chr14:70458400-70464600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr14:70458600-70463800	Weak transcription	Liver	Liver
17	chr14:70458600-70480800	Weak transcription	Brain Germinal Matrix	brain
18	chr14:70458800-70460400	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr14:70458800-70464200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr14:70458800-70465400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr14:70459000-70461400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr14:70459000-70461400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr14:70459000-70484800	Weak transcription	Gastric	stomach
24	chr14:70459200-70460000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr14:70459200-70460000	Genic enhancers	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links