Variant report

Variant	rs12136759
Chromosome Location	chr1:226321051-226321052
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:226318646..226321534-chr1:226372342..226374842,4	MCF-7	breast:
2	chr1:226186376..226188653-chr1:226320391..226323133,2	K562	blood:
3	chr1:226248687..226250856-chr1:226319556..226322520,2	MCF-7	breast:
4	chr1:226318378..226321338-chr1:226323384..226325455,2	MCF-7	breast:
5	chr1:226319376..226322100-chr1:226332829..226335844,3	MCF-7	breast:
6	chr1:226319191..226321532-chr1:226326059..226327998,3	MCF-7	breast:
7	chr1:226312380..226314991-chr1:226319758..226321534,2	K562	blood:
8	chr1:226316368..226319027-chr1:226319079..226321600,2	K562	blood:
9	chr1:226310978..226313880-chr1:226320034..226321559,2	K562	blood:
10	chr1:226308628..226313084-chr1:226318396..226322185,6	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000270598	Chromatin interaction
ENSG00000272562	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000234478	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000182827	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10753418	0.87[MEX][hapmap]
rs10799340	0.83[MEX][hapmap]
rs10915938	0.85[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs10915939	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10915940	0.88[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10915954	0.83[MEX][hapmap]
rs12130296	0.85[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs12145818	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1877153	0.95[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1877155	0.94[ASW][hapmap];1.00[CEU][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1877156	0.87[EUR][1000 genomes]
rs1877161	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2306119	0.87[MEX][hapmap]
rs2306121	0.91[MEX][hapmap]
rs3008192	0.91[MEX][hapmap]
rs35152719	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3887559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4653715	0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4653718	0.82[MEX][hapmap]
rs67947191	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72757092	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7367845	0.87[MEX][hapmap]
rs9286998	0.91[MEX][hapmap]
rs9286999	0.87[MEX][hapmap]
rs9629826	0.87[MEX][hapmap]
rs9645314	1.00[CEU][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9660924	0.91[MEX][hapmap]
rs9728310	0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832747	chr1:226194143-226373415	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
2	nsv873232	chr1:226242772-226375267	Active TSS Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
3	esv1792510	chr1:226277560-226323824	Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv832759	chr1:226303760-226504170	Weak transcription Genic enhancers Enhancers Active TSS Bivalent Enhancer Flanking Active TSS 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 target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12136759	ACBD3	cis	normal skin	skin_eQTL
rs12136759	DUSP10	cis	parietal	SCAN
rs12136759	PARP1	cis	cerebellum	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226310400-226333800	Weak transcription	Small Intestine	intestine
2	chr1:226310600-226322400	Weak transcription	Right Atrium	heart
3	chr1:226310800-226331200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:226313000-226323200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:226313400-226322000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr1:226313400-226322600	Weak transcription	Brain Angular Gyrus	brain
7	chr1:226315600-226322600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr1:226316000-226322000	Enhancers	Primary B cells from cord blood	blood
9	chr1:226316000-226324000	Enhancers	Primary B cells from peripheral blood	blood
10	chr1:226316600-226322600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr1:226316800-226323000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:226317000-226322200	Weak transcription	Fetal Heart	heart
13	chr1:226317200-226331200	Weak transcription	Placenta	Placenta
14	chr1:226318600-226331600	Weak transcription	NH-A	brain
15	chr1:226319400-226321400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:226319400-226321400	Enhancers	GM12878-XiMat	blood
17	chr1:226319400-226324200	Enhancers	Gastric	stomach
18	chr1:226319600-226331200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:226319800-226321400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:226319800-226321400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:226319800-226321600	Enhancers	HepG2	liver
22	chr1:226319800-226321800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:226320000-226321400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr1:226320000-226321600	Enhancers	Placenta Amnion	Placenta Amnion
25	chr1:226320000-226322400	Enhancers	Duodenum Mucosa	Duodenum
26	chr1:226320000-226322600	Weak transcription	Right Ventricle	heart
27	chr1:226320000-226324000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr1:226320000-226324400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:226320400-226321200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
30	chr1:226320400-226321400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr1:226320400-226321400	Enhancers	Lung	lung
32	chr1:226320400-226321600	Enhancers	HMEC	breast
33	chr1:226320400-226322600	Enhancers	Pancreas	Pancrea
34	chr1:226320400-226323200	Enhancers	NHEK	skin
35	chr1:226320600-226321200	Enhancers	Fetal Kidney	kidney
36	chr1:226320600-226321200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr1:226320600-226321200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
38	chr1:226320600-226321200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
39	chr1:226320600-226321200	Enhancers	Spleen	Spleen
40	chr1:226320600-226321200	Enhancers	HSMMtube	muscle
41	chr1:226320600-226321400	Enhancers	HUES6 Cell Line	embryonic stem cell
42	chr1:226320600-226321400	Enhancers	Muscle Satellite Cultured Cells	--
43	chr1:226320600-226322200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr1:226320600-226323800	Enhancers	Fetal Intestine Large	intestine
45	chr1:226320800-226321200	Active TSS	Esophagus	oesophagus
46	chr1:226320800-226321400	Enhancers	H9 Cell Line	embryonic stem cell
47	chr1:226320800-226321400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr1:226320800-226322000	Flanking Active TSS	Stomach Mucosa	stomach
49	chr1:226320800-226322600	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr1:226320800-226322600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links