Variant report

Variant	rs1259359
Chromosome Location	chr12:31741073-31741074
allele	G/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	chr12:31740683-31741315	GM12878	blood:	n/a	n/a
2	POLR2A	chr12:31740754-31741134	Hela-S3	cervix:	n/a	n/a
3	TCF7L2	chr12:31740824-31741172	PANC-1	pancreas:	n/a	n/a
4	POLR2A	chr12:31740732-31741295	HepG2	liver:	n/a	n/a
5	POLR2A	chr12:31737848-31743421	HepG2	liver:	n/a	n/a
6	RUNX3	chr12:31740527-31741137	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:31741015-31741163	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:31740065..31741913-chr12:31741979..31745084,3	K562	blood:
2	chr12:31739424..31741927-chr12:31747863..31749994,2	K562	blood:
3	chr12:31740792..31743101-chr12:31745770..31747885,3	MCF-7	breast:

Variant related genes	Relation type
DENND5B-AS1	TF binding region
ENSG00000170456	Chromatin interaction
ENSG00000252390	Chromatin interaction
ENSG00000255867	Chromatin interaction

Extended variants
information (count: 108 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs1012154	0.82[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap]
rs10743757	0.81[CHB][hapmap]
rs10771832	0.86[CHB][hapmap]
rs10843947	0.86[CHB][hapmap]
rs11051418	0.85[CHB][hapmap]
rs11051441	0.81[CHB][hapmap]
rs11051456	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1150942	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150943	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150945	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150950	0.85[AFR][1000 genomes]
rs1150953	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs1150954	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150955	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150963	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259233	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259235	0.90[CEU][hapmap];0.93[CHB][hapmap];0.83[CHD][hapmap];1.00[LWK][hapmap];0.88[MKK][hapmap];0.85[YRI][hapmap]
rs1259241	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259353	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259354	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259356	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259386	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1259389	0.88[ASN][1000 genomes]
rs1259395	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1259405	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1259409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1259422	0.96[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs1259426	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259428	0.81[CHB][hapmap]
rs1259430	0.84[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs1259435	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1259438	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1259441	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1262390	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1271663	0.88[AFR][1000 genomes]
rs1272773	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1469673	0.86[CHB][hapmap]
rs1542536	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1677154	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1677186	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677187	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1677189	0.81[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1677217	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1716194	0.88[ASN][1000 genomes]
rs1716210	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1716216	1.00[ASW][hapmap];0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs2061761	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2116704	0.86[CHB][hapmap]
rs2568884	0.93[CHB][hapmap]
rs2568885	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2568887	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2604052	0.98[ASN][1000 genomes]
rs2617178	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2617191	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2617200	0.90[CEU][hapmap];0.93[CHB][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes]
rs2682671	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682674	0.86[ASN][1000 genomes]
rs2682677	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2682679	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2682680	0.83[ASN][1000 genomes]
rs2682695	0.87[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2682697	0.84[CHB][hapmap]
rs3850965	0.81[CHB][hapmap]
rs3898368	0.86[CHB][hapmap]
rs4312145	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4482118	0.81[CHB][hapmap]
rs4931501	0.81[CHB][hapmap]
rs4931507	0.81[CHB][hapmap]
rs6487992	0.81[CHB][hapmap]
rs708209	0.86[CHB][hapmap]
rs708212	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs708215	0.81[AMR][1000 genomes]
rs708217	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs7133082	0.81[CHB][hapmap]
rs7135856	0.81[CHB][hapmap]
rs7302698	0.86[CHB][hapmap]
rs7307616	0.81[CHB][hapmap]
rs7313118	0.81[CHB][hapmap]
rs792875	0.81[AMR][1000 genomes]
rs793148	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793149	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs793150	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs793158	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs793161	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes]
rs793171	0.90[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs793173	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793175	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs793176	0.92[CHB][hapmap];0.82[YRI][hapmap]
rs793177	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs793186	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7954595	0.81[CHB][hapmap]
rs7959877	0.86[CHB][hapmap]
rs7962896	0.86[CHB][hapmap]
rs7974437	0.81[CHB][hapmap]
rs7975761	0.86[CHB][hapmap]
rs7976644	0.86[CHB][hapmap]
rs899159	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs976874	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
8	esv1797962	chr12:31733044-31761172	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1259359	DENND5B	cis	parietal	SCAN
rs1259359	PTHLH	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:31721600-31742400	Weak transcription	Aorta	Aorta
2	chr12:31726400-31742000	Weak transcription	Fetal Intestine Large	intestine
3	chr12:31728400-31741800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr12:31732000-31741400	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr12:31732200-31741600	Weak transcription	Fetal Kidney	kidney
6	chr12:31737800-31741800	Flanking Active TSS	GM12878-XiMat	blood
7	chr12:31738400-31742400	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr12:31738400-31742600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr12:31738400-31742600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:31738400-31742600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr12:31738400-31742600	Weak transcription	Lung	lung
12	chr12:31738600-31741200	Weak transcription	Fetal Brain Female	brain
13	chr12:31738600-31741600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr12:31738600-31741600	Weak transcription	Fetal Muscle Leg	muscle
15	chr12:31738600-31741600	Weak transcription	HUVEC	blood vessel
16	chr12:31738600-31741800	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:31738600-31741800	Weak transcription	NHDF-Ad	bronchial
18	chr12:31738600-31742200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr12:31738600-31742400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:31738600-31742400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr12:31738600-31742600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:31738800-31741200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr12:31738800-31741200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr12:31738800-31741200	Weak transcription	Brain Hippocampus Middle	brain
25	chr12:31738800-31741400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr12:31738800-31741400	Weak transcription	Brain Anterior Caudate	brain
27	chr12:31738800-31741600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:31738800-31741600	Weak transcription	Brain Angular Gyrus	brain
29	chr12:31738800-31741800	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr12:31738800-31741800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr12:31738800-31741800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:31738800-31741800	Weak transcription	NHLF	lung
33	chr12:31738800-31742000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:31738800-31742600	Weak transcription	Small Intestine	intestine
35	chr12:31739000-31741600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr12:31739000-31741600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
37	chr12:31739000-31741600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr12:31739000-31741600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:31739000-31741600	Weak transcription	Skeletal Muscle Male	skeletal muscle
40	chr12:31739000-31741600	Weak transcription	Osteobl	bone
41	chr12:31739000-31742000	Weak transcription	HSMM	muscle
42	chr12:31739000-31742000	Weak transcription	NHEK	skin
43	chr12:31739000-31742400	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr12:31739400-31742000	Weak transcription	Fetal Stomach	stomach
45	chr12:31739400-31742400	Enhancers	Stomach Mucosa	stomach
46	chr12:31739800-31742000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:31739800-31742000	Weak transcription	Fetal Intestine Small	intestine
48	chr12:31740000-31742600	Weak transcription	Gastric	stomach
49	chr12:31740200-31741800	Enhancers	Primary B cells from cord blood	blood
50	chr12:31740200-31742200	Enhancers	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links