Variant report

Variant	rs10400435
Chromosome Location	chr12:49726118-49726119
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49725372..49727025-chr12:49731927..49734033,2	MCF-7	breast:
2	chr12:49690361..49691961-chr12:49725710..49727427,2	MCF-7	breast:
3	chr12:49724830..49727128-chr12:49748718..49750720,2	MCF-7	breast:
4	chr12:49680691..49694205-chr12:49725987..49738512,25	K562	blood:
5	chr12:49725096..49726573-chr12:49750546..49751554,11	MCF-7	breast:
6	chr12:49726070..49728754-chr12:49729345..49731828,3	MCF-7	breast:
7	chr12:49725094..49726383-chr12:49741023..49741965,3	MCF-7	breast:
8	chr12:49724052..49726858-chr12:49947435..49949990,2	K562	blood:
9	chr12:49725229..49726134-chr12:49735993..49736894,6	MCF-7	breast:
10	chr12:49725445..49728074-chr12:49906723..49908928,2	MCF-7	breast:
11	chr12:49724272..49727239-chr12:49903612..49905113,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000186897	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000135519	Chromatin interaction
ENSG00000135406	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10400567	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875948	0.91[CEU][hapmap]
rs11168973	0.89[ASN][1000 genomes]
rs11168974	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168975	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.92[ASN][1000 genomes]
rs11168981	0.82[CHB][hapmap]
rs11503617	0.89[ASN][1000 genomes]
rs11835303	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306866	0.82[CHB][hapmap]
rs12313488	0.89[ASN][1000 genomes]
rs12318618	0.91[CEU][hapmap];0.82[MEX][hapmap]
rs12580931	1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.85[ASN][1000 genomes]
rs12581343	1.00[JPT][hapmap]
rs12822293	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2070760	0.85[ASN][1000 genomes]
rs2270741	0.82[CHB][hapmap]
rs28493849	0.85[ASN][1000 genomes]
rs3088008	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4243545	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4898502	0.91[CEU][hapmap];0.82[MEX][hapmap]
rs4898504	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4898519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57241318	0.92[ASN][1000 genomes]
rs59575791	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67236923	0.85[ASN][1000 genomes]
rs67309388	0.85[ASN][1000 genomes]
rs7299812	0.82[CHB][hapmap]
rs73112143	0.85[ASN][1000 genomes]
rs73309977	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7488343	0.85[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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv428801	chr12:49536659-49744884	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
5	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
7	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10400435	PRKAG1	cis	lymphoblastoid	seeQTL
rs10400435	PRPH	cis	cerebellum	SCAN
rs10400435	DDN	cis	parietal	SCAN
rs10400435	TMEM117	cis	cerebellum	SCAN
rs10400435	C1QL4	cis	Thyroid	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49717400-49726800	Weak transcription	Right Atrium	heart
2	chr12:49717800-49727000	Weak transcription	Esophagus	oesophagus
3	chr12:49718000-49726200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr12:49718000-49726400	Weak transcription	Primary B cells from cord blood	blood
5	chr12:49718000-49730200	Weak transcription	Gastric	stomach
6	chr12:49721400-49727000	Weak transcription	NHDF-Ad	bronchial
7	chr12:49721600-49729600	Weak transcription	HSMM	muscle
8	chr12:49721800-49726400	Weak transcription	HUVEC	blood vessel
9	chr12:49724400-49726200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr12:49724400-49727000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr12:49724600-49726400	Genic enhancers	A549	lung
12	chr12:49724600-49727000	Bivalent Enhancer	Fetal Stomach	stomach
13	chr12:49724600-49727000	Weak transcription	Osteobl	bone
14	chr12:49724600-49728800	Weak transcription	GM12878-XiMat	blood
15	chr12:49724800-49726200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr12:49724800-49726200	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:49724800-49726600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr12:49725000-49726200	Bivalent Enhancer	Adipose Nuclei	Adipose
19	chr12:49725000-49726200	Enhancers	Rectal Mucosa Donor 31	rectum
20	chr12:49725000-49726800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr12:49725000-49726800	Bivalent Enhancer	Fetal Muscle Leg	muscle
22	chr12:49725000-49727000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:49725000-49727000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:49725000-49727000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr12:49725000-49728600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr12:49725000-49728600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr12:49725200-49726200	Enhancers	HepG2	liver
28	chr12:49725200-49726400	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr12:49725200-49726800	Weak transcription	HMEC	breast
30	chr12:49725400-49726400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr12:49725400-49726400	Weak transcription	NHEK	skin
32	chr12:49725400-49726600	Enhancers	Placenta	Placenta
33	chr12:49725400-49727000	Weak transcription	NHLF	lung
34	chr12:49725400-49728600	Weak transcription	HSMMtube	muscle
35	chr12:49725400-49730400	Weak transcription	Dnd41	blood
36	chr12:49725600-49726200	Enhancers	Brain Hippocampus Middle	brain
37	chr12:49725600-49726200	Bivalent Enhancer	Fetal Intestine Small	intestine
38	chr12:49725600-49726400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr12:49725600-49726800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:49725600-49727000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
41	chr12:49725600-49728000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr12:49725800-49726400	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr12:49725800-49726600	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:49725800-49726600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr12:49725800-49730400	Weak transcription	Hela-S3	cervix
46	chr12:49726000-49726200	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
47	chr12:49726000-49726400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr12:49726000-49726600	Bivalent Enhancer	Brain Germinal Matrix	brain
49	chr12:49726000-49726800	Weak transcription	Liver	Liver
50	chr12:49726000-49727000	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle

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