Variant report

Variant	rs781665
Chromosome Location	chr4:57831461-57831462
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	POLR2A	chr4:57831382-57831500	HepG2	liver:	n/a	n/a
2	POLR2A	chr4:57831326-57831479	H1-hESC	embryonic stem cell:	n/a	n/a
3	ZBTB33	chr4:57831233-57831515	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:149223629..149225361-chr4:57830063..57832161,2	MCF-7	breast:
2	chr4:57830075..57832826-chr4:57843564..57845499,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269949	TF binding region
ENSG00000084092	Chromatin interaction
ENSG00000206737	Chromatin interaction
ENSG00000047315	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10866441	0.81[ASN][1000 genomes]
rs1107675	0.93[ASN][1000 genomes]
rs11729152	0.88[ASN][1000 genomes]
rs11735158	0.83[ASN][1000 genomes]
rs11736192	0.81[ASN][1000 genomes]
rs11736808	0.84[ASN][1000 genomes]
rs11932673	0.93[ASN][1000 genomes]
rs12501224	0.81[ASN][1000 genomes]
rs12502076	0.81[ASN][1000 genomes]
rs1277271	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1277284	0.83[EUR][1000 genomes]
rs1277287	0.88[ASN][1000 genomes]
rs1277288	0.88[ASN][1000 genomes]
rs13121176	0.88[ASN][1000 genomes]
rs13136432	0.81[ASN][1000 genomes]
rs1315005	0.88[ASN][1000 genomes]
rs13150593	0.81[ASN][1000 genomes]
rs1625691	0.88[ASN][1000 genomes]
rs17087307	0.93[ASN][1000 genomes]
rs17087317	0.93[ASN][1000 genomes]
rs1713994	0.83[ASN][1000 genomes]
rs1718839	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1718886	0.83[EUR][1000 genomes]
rs1976780	0.93[ASN][1000 genomes]
rs2228991	0.88[ASN][1000 genomes]
rs2948348	0.84[EUR][1000 genomes]
rs34124552	0.81[ASN][1000 genomes]
rs34448457	0.81[ASN][1000 genomes]
rs34576794	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34659774	0.93[ASN][1000 genomes]
rs35267092	0.81[ASN][1000 genomes]
rs35982175	0.86[EUR][1000 genomes]
rs3733306	0.87[ASN][1000 genomes]
rs3796528	0.88[ASN][1000 genomes]
rs62308155	0.80[ASN][1000 genomes]
rs6554399	0.88[ASN][1000 genomes]
rs6816457	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs73242616	0.86[ASN][1000 genomes]
rs7668814	0.84[AFR][1000 genomes]
rs7685576	0.86[ASN][1000 genomes]
rs781666	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs781668	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9942208	0.93[ASN][1000 genomes]
rs9996331	0.85[AFR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv1012287	chr4:57652778-57853485	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv1012125	chr4:57668229-57865803	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57793600-57842000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr4:57793600-57842000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr4:57820200-57836000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr4:57820200-57836000	Weak transcription	Esophagus	oesophagus
5	chr4:57821600-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr4:57822600-57832600	Weak transcription	Fetal Brain Male	brain
7	chr4:57824600-57838400	Weak transcription	Aorta	Aorta
8	chr4:57825200-57832400	Weak transcription	A549	lung
9	chr4:57825600-57832200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr4:57825600-57832600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr4:57825600-57838600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr4:57826000-57832000	Weak transcription	Psoas Muscle	Psoas
13	chr4:57826400-57831800	Weak transcription	Gastric	stomach
14	chr4:57826400-57839800	Strong transcription	Primary T cells from cord blood	blood
15	chr4:57826600-57832200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
16	chr4:57826600-57833400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:57826600-57834400	Strong transcription	Fetal Muscle Trunk	muscle
18	chr4:57826600-57834600	Strong transcription	Fetal Stomach	stomach
19	chr4:57826600-57835200	Strong transcription	Brain Anterior Caudate	brain
20	chr4:57826600-57838600	Strong transcription	Fetal Intestine Small	intestine
21	chr4:57826600-57838800	Strong transcription	Liver	Liver
22	chr4:57826600-57839000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr4:57826600-57839200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr4:57826600-57840800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr4:57826600-57840800	Strong transcription	Fetal Brain Female	brain
26	chr4:57826600-57840800	Strong transcription	Fetal Muscle Leg	muscle
27	chr4:57826600-57840800	Strong transcription	Fetal Thymus	thymus
28	chr4:57826600-57841000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr4:57826600-57841400	Strong transcription	Fetal Intestine Large	intestine
30	chr4:57826800-57839000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:57826800-57840800	Strong transcription	HUES64 Cell Line	embryonic stem cell
32	chr4:57826800-57840800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr4:57826800-57840800	Weak transcription	Stomach Mucosa	stomach
34	chr4:57827000-57832800	Strong transcription	Brain Cingulate Gyrus	brain
35	chr4:57827000-57838400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr4:57827000-57840400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:57827000-57843200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr4:57827200-57832600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr4:57827200-57833600	Strong transcription	Thymus	Thymus
40	chr4:57827200-57835200	Strong transcription	Brain Inferior Temporal Lobe	brain
41	chr4:57827200-57835400	Strong transcription	Duodenum Smooth Muscle	Duodenum
42	chr4:57827200-57838400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr4:57827200-57838800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr4:57827200-57839000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr4:57827200-57840200	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr4:57827200-57840400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
47	chr4:57827200-57840400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr4:57827200-57840600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr4:57827200-57840800	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr4:57827200-57840800	Strong transcription	Dnd41	blood

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