Variant report

Variant	rs4757446
Chromosome Location	chr11:16948199-16948200
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:16947090..16949629-chr11:17095736..17097514,2	MCF-7	breast:
2	chr11:16946793..16948459-chr14:74981920..74983438,2	MCF-7	breast:
3	chr11:16939336..16941584-chr11:16944195..16948360,3	K562	blood:
4	chr11:16946724..16949715-chr11:17035488..17037274,2	MCF-7	breast:
5	chr11:16947021..16948883-chr11:16954083..16956444,2	MCF-7	breast:
6	chr11:16947321..16948978-chr11:17097717..17099259,2	MCF-7	breast:
7	chr11:16945639..16949520-chr11:16949584..16951727,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272034	Chromatin interaction
ENSG00000201403	Chromatin interaction
ENSG00000110700	Chromatin interaction
ENSG00000184669	Chromatin interaction
ENSG00000166689	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10741716	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10766354	0.86[CHB][hapmap]
rs10766356	0.80[CEU][hapmap];0.87[CHB][hapmap]
rs10766359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10832695	0.87[CHB][hapmap]
rs11024074	0.84[JPT][hapmap]
rs11024076	0.80[CEU][hapmap]
rs11829035	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12221693	0.92[ASN][1000 genomes]
rs2041236	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.80[GIH][hapmap];0.84[JPT][hapmap]
rs2215085	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs365215	0.81[ASN][1000 genomes]
rs370161	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap]
rs378755	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap]
rs382734	0.81[CHD][hapmap]
rs402973	0.80[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.92[MEX][hapmap]
rs415300	0.81[CHD][hapmap]
rs416258	0.83[JPT][hapmap]
rs432373	0.87[CHB][hapmap]
rs442389	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4756878	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs4757444	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4757453	0.87[ASN][1000 genomes]
rs55646909	0.90[ASN][1000 genomes]
rs7117737	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7117745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7121911	0.93[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7481080	0.84[CEU][hapmap];0.83[CHB][hapmap];0.85[GIH][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7925386	0.92[ASN][1000 genomes]
rs7931794	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs982550	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs982551	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	nsv832077	chr11:16834545-17059176	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv7689	chr11:16945953-16990852	Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4757446	TEAD1	cis	parietal	SCAN
rs4757446	HPS5	cis	parietal	SCAN
rs4757446	ZNF839	trans	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:16947200-16948600	Bivalent Enhancer	Placenta	Placenta
2	chr11:16947200-16948800	Flanking Active TSS	Hela-S3	cervix
3	chr11:16947400-16948600	Bivalent Enhancer	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr11:16947400-16948600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
5	chr11:16947400-16948600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr11:16947600-16948200	Bivalent Enhancer	Primary B cells from cord blood	blood
7	chr11:16947600-16948200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
8	chr11:16947600-16948200	Flanking Active TSS	Fetal Heart	heart
9	chr11:16947600-16948400	Enhancers	Liver	Liver
10	chr11:16947600-16948400	Enhancers	Placenta Amnion	Placenta Amnion
11	chr11:16947600-16948400	Enhancers	Spleen	Spleen
12	chr11:16947600-16948600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr11:16947600-16948600	Bivalent Enhancer	Fetal Lung	lung
14	chr11:16947600-16948600	Enhancers	Right Ventricle	heart
15	chr11:16947600-16955400	Weak transcription	Gastric	stomach
16	chr11:16947800-16948200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr11:16947800-16948200	Bivalent Enhancer	Fetal Intestine Small	intestine
18	chr11:16947800-16948200	Enhancers	A549	lung
19	chr11:16947800-16948400	Bivalent Enhancer	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:16947800-16948400	Enhancers	Esophagus	oesophagus
21	chr11:16947800-16948400	Enhancers	Fetal Intestine Large	intestine
22	chr11:16947800-16948400	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
23	chr11:16947800-16948400	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr11:16947800-16948600	Enhancers	Left Ventricle	heart
25	chr11:16947800-16948600	Enhancers	Right Atrium	heart
26	chr11:16947800-16949200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:16947800-16949400	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
28	chr11:16947800-16949400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
29	chr11:16947800-16949400	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr11:16947800-16949800	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr11:16947800-16951200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr11:16947800-16954200	Weak transcription	Pancreas	Pancrea
33	chr11:16948000-16948200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr11:16948000-16948200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
35	chr11:16948000-16948200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:16948000-16948200	Enhancers	Brain Anterior Caudate	brain
37	chr11:16948000-16948200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr11:16948000-16948400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
39	chr11:16948000-16948400	Enhancers	HepG2	liver
40	chr11:16948000-16948600	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
41	chr11:16948000-16949200	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
42	chr11:16948000-16949400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
43	chr11:16948000-16954200	Weak transcription	Ovary	ovary

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