Variant report

Variant	rs1259355
Chromosome Location	chr12:31688535-31688536
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	RAD21	chr12:31688376-31688713	H1-hESC	embryonic stem cell:	n/a	n/a

Variant related genes	Relation type
ENSG00000225349	TF binding region

Extended variants
information (count: 82 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1012154	0.81[ASN][1000 genomes]
rs10743757	0.89[ASN][1000 genomes]
rs10743759	0.94[ASN][1000 genomes]
rs10771832	0.83[ASN][1000 genomes]
rs10771838	0.87[ASN][1000 genomes]
rs10771843	0.94[ASN][1000 genomes]
rs10771844	0.85[ASN][1000 genomes]
rs10771845	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10771846	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10843942	0.81[ASN][1000 genomes]
rs10843958	0.89[ASN][1000 genomes]
rs10843959	0.89[ASN][1000 genomes]
rs10843963	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11051435	0.87[ASN][1000 genomes]
rs11051437	0.87[ASN][1000 genomes]
rs11051439	0.87[ASN][1000 genomes]
rs11051441	0.89[ASN][1000 genomes]
rs1150950	0.84[ASN][1000 genomes]
rs1150953	0.84[ASN][1000 genomes]
rs1259235	0.81[ASN][1000 genomes]
rs1259386	0.84[AFR][1000 genomes]
rs1259401	0.82[ASN][1000 genomes]
rs1259427	0.84[ASN][1000 genomes]
rs1259428	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259430	0.83[ASN][1000 genomes]
rs1259432	0.94[ASN][1000 genomes]
rs1271128	0.99[ASN][1000 genomes]
rs1271663	0.84[ASN][1000 genomes]
rs1996693	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2352048	0.87[ASN][1000 genomes]
rs2568884	0.80[ASN][1000 genomes]
rs2604052	0.84[AFR][1000 genomes]
rs2617190	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2617200	0.84[ASN][1000 genomes]
rs2682674	0.82[AFR][1000 genomes]
rs2682697	0.82[AFR][1000 genomes]
rs2682700	0.85[AFR][1000 genomes]
rs3803113	0.87[ASN][1000 genomes]
rs3844573	0.89[ASN][1000 genomes]
rs3850965	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3898368	0.87[ASN][1000 genomes]
rs4482118	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4930980	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4931501	0.89[ASN][1000 genomes]
rs4931506	0.88[ASN][1000 genomes]
rs4931507	0.89[ASN][1000 genomes]
rs6416254	0.81[ASN][1000 genomes]
rs6487992	0.89[ASN][1000 genomes]
rs708209	0.85[AFR][1000 genomes]
rs7133082	0.88[ASN][1000 genomes]
rs7135856	0.88[ASN][1000 genomes]
rs7136476	0.94[ASN][1000 genomes]
rs7136943	0.89[ASN][1000 genomes]
rs7137406	0.89[ASN][1000 genomes]
rs7302698	0.81[ASN][1000 genomes]
rs7307593	0.94[ASN][1000 genomes]
rs7307616	0.94[ASN][1000 genomes]
rs7313118	0.89[ASN][1000 genomes]
rs7313689	0.83[ASN][1000 genomes]
rs7314417	0.83[ASN][1000 genomes]
rs793154	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs793157	0.85[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs793176	0.81[ASN][1000 genomes]
rs793180	0.82[AFR][1000 genomes]
rs793184	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7954023	0.89[ASN][1000 genomes]
rs7954595	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7959877	0.83[ASN][1000 genomes]
rs7962896	0.83[ASN][1000 genomes]
rs7963161	0.82[ASN][1000 genomes]
rs7967832	0.86[ASN][1000 genomes]
rs7974437	0.85[ASN][1000 genomes]
rs7976644	0.84[ASN][1000 genomes]
rs7977453	0.89[ASN][1000 genomes]
rs9738834	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041877	chr12:31009451-31809254	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv541440	chr12:31009451-31809254	ZNF genes & repeats Enhancers Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
3	esv1836923	chr12:31539122-31761172	Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	esv2760267	chr12:31626732-31909908	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
5	nsv898965	chr12:31631819-31771689	Enhancers Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv832365	chr12:31642811-31808532	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	esv1842653	chr12:31670378-31744033	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31675600-31689000	Weak transcription	Small Intestine	intestine
2	chr12:31679000-31688800	Weak transcription	Psoas Muscle	Psoas
3	chr12:31679000-31691400	Weak transcription	Fetal Intestine Large	intestine
4	chr12:31679800-31692000	Weak transcription	GM12878-XiMat	blood
5	chr12:31681200-31691000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr12:31681200-31691600	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:31684800-31690600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr12:31685200-31688800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:31685400-31691000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr12:31685400-31691600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:31685400-31700600	Weak transcription	Aorta	Aorta
12	chr12:31685400-31708600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr12:31685600-31690000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:31686600-31688800	Weak transcription	Adipose Nuclei	Adipose
15	chr12:31686800-31688800	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:31686800-31689000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr12:31686800-31689400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr12:31686800-31689400	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr12:31686800-31689600	Weak transcription	Liver	Liver
20	chr12:31686800-31689800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:31686800-31690400	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr12:31686800-31693200	Weak transcription	Fetal Intestine Small	intestine
23	chr12:31686800-31695600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr12:31687000-31689000	Weak transcription	Hela-S3	cervix
25	chr12:31687000-31689600	Weak transcription	HepG2	liver
26	chr12:31687000-31691200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr12:31687000-31691400	Weak transcription	Brain Anterior Caudate	brain
28	chr12:31687600-31689000	Strong transcription	Primary B cells from cord blood	blood
29	chr12:31687600-31689000	Genic enhancers	A549	lung
30	chr12:31687800-31689000	Enhancers	Left Ventricle	heart
31	chr12:31687800-31689000	Enhancers	Right Atrium	heart
32	chr12:31688000-31689000	Genic enhancers	Primary B cells from peripheral blood	blood
33	chr12:31688200-31688600	Enhancers	Fetal Heart	heart
34	chr12:31688200-31688800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:31688200-31689000	Enhancers	Right Ventricle	heart
36	chr12:31688200-31690400	Weak transcription	Duodenum Mucosa	Duodenum
37	chr12:31688400-31688600	Enhancers	H9 Cell Line	embryonic stem cell
38	chr12:31688400-31688800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:31688400-31689200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr12:31688400-31689200	Enhancers	Ovary	ovary
41	chr12:31688400-31690000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

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