Variant report

Variant	rs766974
Chromosome Location	chr13:111217422-111217423
allele	C/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	TCF12	chr13:111217138-111218243	ECC-1	luminal epithelium:	n/a	chr13:111217322-111217332
2	NFIC	chr13:111217405-111218235	ECC-1	luminal epithelium:	n/a	n/a
3	TEAD4	chr13:111216927-111218090	ECC-1	luminal epithelium:	n/a	n/a
4	TCF12	chr13:111217043-111218229	ECC-1	luminal epithelium:	n/a	chr13:111217322-111217332
5	MAX	chr13:111216778-111218103	ECC-1	luminal epithelium:	n/a	chr13:111216837-111216847
6	EP300	chr13:111216807-111218250	ECC-1	luminal epithelium:	n/a	chr13:111217925-111217935
7	USF2	chr13:111217417-111217665	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOXM1	chr13:111217342-111218306	ECC-1	luminal epithelium:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:111217228..111219179-chr13:111567056..111569002,2	MCF-7	breast:
2	chr13:111205877..111207739-chr13:111217049..111218978,2	K562	blood:
3	chr13:111215515..111217853-chr13:111220246..111222772,2	K562	blood:
4	chr13:111214986..111217647-chr13:111218744..111220287,2	MCF-7	breast:

Variant related genes	Relation type
RAB20	TF binding region
ENSG00000088448	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12873717	0.84[ASN][1000 genomes]
rs389685	0.82[JPT][hapmap]
rs67721460	0.91[ASN][1000 genomes]
rs7984766	0.82[ASN][1000 genomes]
rs9521843	0.91[ASN][1000 genomes]
rs9521844	1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs9521845	0.82[JPT][hapmap]
rs9588192	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
6	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
7	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS 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	25 gene(s)	inside rSNPs	diseases
9	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs766974	RAB20	cis	lymphoblastoid	seeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111214800-111218600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr13:111214800-111226400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr13:111215200-111220000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr13:111215400-111218200	Weak transcription	Psoas Muscle	Psoas
5	chr13:111215400-111221000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr13:111215600-111222600	Weak transcription	Ovary	ovary
7	chr13:111215800-111219800	Weak transcription	Placenta	Placenta
8	chr13:111215800-111220000	Weak transcription	Small Intestine	intestine
9	chr13:111215800-111220800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr13:111216000-111220000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr13:111216000-111220000	Weak transcription	Stomach Smooth Muscle	stomach
12	chr13:111216000-111220600	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr13:111216000-111227800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr13:111216000-111227800	Weak transcription	Gastric	stomach
15	chr13:111216200-111217600	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr13:111216200-111219000	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr13:111216200-111219800	Weak transcription	K562	blood
18	chr13:111216200-111220800	Weak transcription	Adipose Nuclei	Adipose
19	chr13:111216200-111221000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr13:111216200-111221600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr13:111216200-111223200	Weak transcription	Duodenum Smooth Muscle	Duodenum
22	chr13:111216200-111226400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr13:111216600-111218800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
24	chr13:111216600-111223000	Weak transcription	Fetal Intestine Small	intestine
25	chr13:111216800-111218000	Enhancers	Hela-S3	cervix
26	chr13:111217000-111217600	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr13:111217000-111217600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
28	chr13:111217000-111217800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr13:111217000-111217800	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr13:111217000-111217800	Enhancers	Fetal Intestine Large	intestine
31	chr13:111217000-111218000	Enhancers	Fetal Kidney	kidney
32	chr13:111217200-111217800	Enhancers	HUES64 Cell Line	embryonic stem cell
33	chr13:111217200-111217800	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr13:111217200-111218000	Weak transcription	Fetal Stomach	stomach
35	chr13:111217200-111227600	Weak transcription	Spleen	Spleen
36	chr13:111217200-111227800	Weak transcription	Pancreas	Pancrea
37	chr13:111217400-111217800	Enhancers	H1 Cell Line	embryonic stem cell
38	chr13:111217400-111217800	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr13:111217400-111218800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr13:111217400-111221200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:111217400-111227400	Weak transcription	H9 Cell Line	embryonic stem cell

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