Variant report

Variant	rs11575334
Chromosome Location	chr7:50597301-50597302
allele	C/T
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	EP300	chr7:50597088-50601096	SK-N-SH	brain:	n/a	chr7:50599946-50599960 chr7:50597383-50597399

Variant related genes	Relation type
ENSG00000226122	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10499694	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11575352	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11575356	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11765748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11767334	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12538938	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12718583	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1470749	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4947644	0.85[CEU][hapmap];0.86[YRI][hapmap];0.84[EUR][1000 genomes]
rs6975453	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7778349	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7781950	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7786398	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs7792578	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs998850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1016665	chr7:50452552-51404524	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv888021	chr7:50538589-50610071	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1015758	chr7:50565404-50768153	Flanking Active TSS Genic enhancers Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv1023228	chr7:50573214-50777634	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11575334	FIGNL1	cis	Thyroid	GTEx
rs11575334	FIGNL1	cis	Skin Sun Exposed Lower leg	GTEx
rs11575334	FIGNL1	cis	lung	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:50565200-50609000	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr7:50589000-50599200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:50595200-50600000	Enhancers	Pancreas	Pancrea
4	chr7:50595200-50604600	Genic enhancers	Fetal Intestine Small	intestine
5	chr7:50595800-50597400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr7:50595800-50599400	Enhancers	Fetal Intestine Large	intestine
7	chr7:50596000-50597400	Enhancers	Duodenum Mucosa	Duodenum
8	chr7:50596000-50597800	Enhancers	Stomach Mucosa	stomach
9	chr7:50596200-50598200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr7:50596200-50598800	Weak transcription	Brain Germinal Matrix	brain
11	chr7:50596200-50599000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr7:50596200-50599000	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr7:50596200-50599200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr7:50596400-50597400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:50596400-50599000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr7:50596800-50598600	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr7:50596800-50599000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr7:50597000-50597800	Enhancers	HepG2	liver
19	chr7:50597000-50598800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr7:50597000-50599000	Weak transcription	Gastric	stomach
21	chr7:50597000-50601200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr7:50597000-50601400	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr7:50597200-50597400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr7:50597200-50603600	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links