Variant report

Variant	rs13107767
Chromosome Location	chr4:48045691-48045692
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:48018543..48020121-chr4:48043793..48046506,2	MCF-7	breast:
2	chr4:48043679..48046228-chr4:48047228..48049577,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198515	Chromatin interaction
ENSG00000163293	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10517204	0.87[JPT][hapmap]
rs10805163	0.87[JPT][hapmap]
rs1396051	0.87[JPT][hapmap]
rs1507925	0.84[ASN][1000 genomes]
rs2230594	0.82[ASN][1000 genomes]
rs28650378	0.81[ASN][1000 genomes]
rs28667740	0.83[ASN][1000 genomes]
rs33964061	0.82[ASN][1000 genomes]
rs3805187	0.86[CHB][hapmap];0.95[JPT][hapmap]
rs4340770	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4694880	0.87[JPT][hapmap]
rs4695332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6447610	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6447611	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6447612	0.81[ASN][1000 genomes]
rs6447613	0.81[ASN][1000 genomes]
rs6447614	0.82[ASN][1000 genomes]
rs6829490	0.81[ASN][1000 genomes]
rs6839501	0.81[ASN][1000 genomes]
rs906487	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996535	0.95[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]

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	esv3447039	chr4:47822266-48285222	Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
2	nsv1013947	chr4:47915527-48052824	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv537082	chr4:47915527-48052824	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1006745	chr4:47935250-48052824	Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv537083	chr4:47935250-48052824	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13107767	CNGA1	cis	Adipose Subcutaneous	GTEx
rs13107767	TXK	cis	parietal	SCAN
rs13107767	TEC	cis	parietal	SCAN
rs13107767	CNGA1	cis	Muscle Skeletal	GTEx

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:48019800-48049800	Weak transcription	Esophagus	oesophagus
2	chr4:48020600-48049600	Weak transcription	Colonic Mucosa	Colon
3	chr4:48034200-48049600	Weak transcription	Pancreas	Pancrea
4	chr4:48036400-48046400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr4:48038000-48047800	Weak transcription	NHEK	skin
6	chr4:48038600-48053000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr4:48041600-48053000	Weak transcription	HMEC	breast
8	chr4:48043800-48045800	Flanking Active TSS	GM12878-XiMat	blood
9	chr4:48044200-48045800	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr4:48044200-48045800	Enhancers	Sigmoid Colon	Sigmoid Colon
11	chr4:48044400-48045800	Enhancers	Fetal Intestine Large	intestine
12	chr4:48044400-48046600	Enhancers	Primary B cells from peripheral blood	blood
13	chr4:48044600-48046000	Enhancers	Fetal Intestine Small	intestine
14	chr4:48044600-48049200	Enhancers	Primary B cells from cord blood	blood
15	chr4:48044800-48046000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:48044800-48049200	Enhancers	Primary T helper cells PMA-I stimulated	--
17	chr4:48044800-48049400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr4:48045000-48045800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr4:48045000-48047200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr4:48045000-48049200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr4:48045000-48049400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr4:48045000-48049400	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr4:48045200-48045800	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
24	chr4:48045200-48048200	Enhancers	Stomach Mucosa	stomach
25	chr4:48045200-48049000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:48045400-48045800	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr4:48045400-48045800	Enhancers	Placenta Amnion	Placenta Amnion
28	chr4:48045400-48052200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr4:48045600-48045800	Enhancers	H9 Cell Line	embryonic stem cell
30	chr4:48045600-48045800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr4:48045600-48046000	Enhancers	Liver	Liver
32	chr4:48045600-48046000	Enhancers	HepG2	liver
33	chr4:48045600-48046400	Weak transcription	Primary T cells from cord blood	blood
34	chr4:48045600-48047800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr4:48045600-48048200	Weak transcription	Primary hematopoietic stem cells	blood
36	chr4:48045600-48048200	Weak transcription	Fetal Heart	heart

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