Variant report

Variant	rs1029629
Chromosome Location	chr12:1799267-1799268
allele	A/C
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	JUN	chr12:1799030-1801092	K562	blood:	n/a	chr12:1800125-1800134 chr12:1800811-1800823
2	POLR2A	chr12:1799201-1801657	MCF10A-Er-Src	breast:	n/a	n/a
3	POLR2A	chr12:1799185-1800944	Raji	blood:	n/a	n/a
4	POLR2A	chr12:1799214-1801006	PBDE	blood:	n/a	n/a
5	SREBP1	chr12:1798919-1802146	GM12878	blood:	n/a	n/a
6	POLR2A	chr12:1799240-1801090	Hela-S3	cervix:	n/a	n/a
7	HCFC1	chr12:1798998-1801457	Hela-S3	cervix:	n/a	n/a
8	MAZ	chr12:1798841-1801165	IMR90	lung:	n/a	chr12:1799900-1799910 chr12:1800352-1800359
9	POLR2A	chr12:1799091-1801940	MCF10A-Er-Src	breast:	n/a	n/a
10	POLR2A	chr12:1799219-1799542	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
2	chr12:1769387..1773191-chr12:1797591..1801415,7	K562	blood:
3	chr12:1797794..1800188-chr12:1882818..1885035,2	MCF-7	breast:
4	chr12:1798163..1800510-chr12:1865299..1867613,2	K562	blood:
5	chr12:1768367..1774746-chr12:1797764..1801789,11	MCF-7	breast:

Variant related genes	Relation type
ADIPOR2	TF binding region
ENSG00000243663	Chromatin interaction
ENSG00000266043	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10773982	0.87[CEU][hapmap];0.80[MEX][hapmap]
rs10848551	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10848552	0.99[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10848553	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10848558	0.85[AMR][1000 genomes]
rs11061918	0.87[CHD][hapmap];0.85[JPT][hapmap];0.82[ASN][1000 genomes]
rs11061919	0.84[AMR][1000 genomes]
rs11061920	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061921	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061923	0.81[AMR][1000 genomes]
rs11061924	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061925	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061927	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061935	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs11061937	0.82[CEU][hapmap];0.86[MEX][hapmap];0.81[AMR][1000 genomes]
rs11061940	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11061946	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs11061952	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs11061957	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061962	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11061967	0.80[CHB][hapmap]
rs11061973	0.80[CHB][hapmap]
rs1136213	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11832817	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12230440	0.80[CHB][hapmap];0.82[CHD][hapmap]
rs12230579	0.82[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12231894	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342	0.87[MEX][hapmap]
rs12582624	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12810020	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12821401	0.80[CHB][hapmap]
rs12828908	0.87[MEX][hapmap]
rs12831353	0.87[MEX][hapmap]
rs2058033	0.80[CHB][hapmap];0.87[CHD][hapmap]
rs2058034	0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2058035	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2370055	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34375871	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4766413	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6489320	0.99[ASN][1000 genomes]
rs6489323	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6489324	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66590925	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7132033	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7297509	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7975826	0.84[AMR][1000 genomes]
rs7978818	0.83[CEU][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs929434	0.87[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1029629	DNAJC15	trans	lymphoblastoid	seeQTL

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1796600-1799400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:1797400-1799600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr12:1799000-1799400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr12:1799000-1799400	Enhancers	Primary T cells from cord blood	blood
5	chr12:1799000-1799400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:1799000-1799400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr12:1799000-1799400	Flanking Active TSS	K562	blood
8	chr12:1799000-1799400	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr12:1799000-1799400	Enhancers	NHEK	skin
10	chr12:1799000-1799600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr12:1799000-1799600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
12	chr12:1799000-1799600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:1799000-1799600	Enhancers	Primary T helper naive cells from peripheral blood	blood
14	chr12:1799000-1799600	Flanking Active TSS	Dnd41	blood
15	chr12:1799200-1799400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:1799200-1799400	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr12:1799200-1799400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:1799200-1799400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr12:1799200-1799400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:1799200-1799400	Enhancers	Primary hematopoietic stem cells	blood
21	chr12:1799200-1799400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr12:1799200-1799400	Active TSS	Primary T killer memory cells from peripheral blood	blood
23	chr12:1799200-1799400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:1799200-1799400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:1799200-1799400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:1799200-1799400	Enhancers	Adipose Nuclei	Adipose
27	chr12:1799200-1799400	Enhancers	Liver	Liver
28	chr12:1799200-1799400	Enhancers	Brain Angular Gyrus	brain
29	chr12:1799200-1799400	Enhancers	Brain Anterior Caudate	brain
30	chr12:1799200-1799400	Enhancers	Brain Hippocampus Middle	brain
31	chr12:1799200-1799400	Enhancers	Brain Inferior Temporal Lobe	brain
32	chr12:1799200-1799400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:1799200-1799400	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr12:1799200-1799400	Flanking Active TSS	Fetal Brain Male	brain
35	chr12:1799200-1799400	Enhancers	Fetal Heart	heart
36	chr12:1799200-1799400	Flanking Active TSS	Fetal Intestine Small	intestine
37	chr12:1799200-1799400	Enhancers	Fetal Muscle Leg	muscle
38	chr12:1799200-1799400	Enhancers	Fetal Thymus	thymus
39	chr12:1799200-1799400	Enhancers	Rectal Mucosa Donor 29	rectum
40	chr12:1799200-1799400	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr12:1799200-1799400	Enhancers	Stomach Mucosa	stomach
42	chr12:1799200-1799400	Flanking Active TSS	HepG2	liver
43	chr12:1799200-1799400	Flanking Active TSS	NHDF-Ad	bronchial
44	chr12:1799200-1799600	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:1799200-1799600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
46	chr12:1799200-1799600	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
47	chr12:1799200-1799600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:1799200-1799600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr12:1799200-1799600	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr12:1799200-1799600	Enhancers	Primary B cells from cord blood	blood

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