Variant report

Variant	rs3138139
Chromosome Location	chr12:56115883-56115884
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56114860-56116296	HUVEC	blood vessel:	n/a	n/a
2	POLR2A	chr12:56115714-56116003	SK-N-SH	brain:	n/a	n/a
3	POLR2A	chr12:56113532-56124497	U87	brain:	n/a	n/a
4	POLR2A	chr12:56114616-56115992	ECC-1	luminal epithelium:	n/a	n/a
5	BCL3	chr12:56114552-56115889	A549	lung:	n/a	chr12:56114576-56114585 chr12:56115419-56115427
6	POLR2A	chr12:56114542-56115895	SK-N-SH	brain:	n/a	n/a
7	POLR2A	chr12:56114862-56115942	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr12:56113762-56120156	U87	brain:	n/a	n/a
9	POLR2A	chr12:56113762-56116080	U87	brain:	n/a	n/a
10	POLR2A	chr12:56115127-56115911	PFSK-1	brain:	n/a	n/a
11	POLR2A	chr12:56114602-56115925	ProgFib	skin:	n/a	n/a
12	POLR2A	chr12:56115821-56116037	K562	blood:	n/a	n/a
13	POLR2A	chr12:56115633-56115995	MCF10A-Er-Src	breast:	n/a	n/a
14	RCOR1	chr12:56113463-56116004	IMR90	lung:	n/a	n/a
15	POLR2A	chr12:56114778-56116098	PANC-1	pancreas:	n/a	n/a
16	POLR2A	chr12:56114692-56118824	IMR90	lung:	n/a	n/a
17	POLR2A	chr12:56113243-56124503	U87	brain:	n/a	n/a
18	POLR2A	chr12:56114576-56116003	HUVEC	blood vessel:	n/a	n/a
19	POLR2A	chr12:56114703-56116026	SK-N-MC	brain:	n/a	n/a
20	POLR2A	chr12:56114636-56115950	HUVEC	blood vessel:	n/a	n/a
21	POLR2A	chr12:56115663-56115925	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr12:56114833-56115955	A549	lung:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:56087401..56089684-chr12:56115216..56116747,2	MCF-7	breast:
2	chr12:56113979..56116448-chr12:56136696..56138378,2	MCF-7	breast:
3	chr12:56115003..56117431-chr12:56512002..56513619,2	MCF-7	breast:
4	chr12:56055852..56057632-chr12:56114963..56117195,2	MCF-7	breast:
5	chr12:56048123..56050155-chr12:56113655..56116365,3	MCF-7	breast:
6	chr12:56075054..56077566-chr12:56115620..56119645,3	MCF-7	breast:
7	chr12:56115280..56117661-chr12:56434487..56437125,2	MCF-7	breast:
8	chr12:56040086..56042095-chr12:56114770..56116489,2	MCF-7	breast:

No data

Variant related genes	Relation type
RDH5	TF binding region
ENSG00000139641	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000197728	Chromatin interaction
ENSG00000270458	Chromatin interaction
ENSG00000257449	Chromatin interaction
ENSG00000258907	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000170439	Chromatin interaction
ENSG00000272837	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs1081732	1.00[CEU][hapmap]
rs3138132	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3138140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs772254	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs772262	0.87[CEU][hapmap]
rs7965333	1.00[CEU][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	nsv948625	chr12:55838718-56118833	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv525231	chr12:56076919-56124332	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
3	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
4	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3138139	KRT73	cis	cerebellum	SCAN
rs3138139	CD63	cis	lymphoblastoid	seeQTL
rs3138139	BLOC1S1	cis	lymphoblastoid	seeQTL
rs3138139	MIP	cis	cerebellum	SCAN
rs3138139	INHBC	cis	parietal	SCAN
rs3138139	KRT2	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56111200-56120400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr12:56111600-56118400	Strong transcription	Thymus	Thymus
3	chr12:56112000-56117800	Weak transcription	Primary hematopoietic stem cells	blood
4	chr12:56112200-56116600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr12:56112200-56118000	Weak transcription	Fetal Lung	lung
6	chr12:56112400-56118000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr12:56112600-56117600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:56112600-56118200	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr12:56112600-56118800	Weak transcription	Small Intestine	intestine
10	chr12:56112800-56116800	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:56112800-56116800	Weak transcription	HUES64 Cell Line	embryonic stem cell
12	chr12:56112800-56117200	Strong transcription	Primary T cells from cord blood	blood
13	chr12:56112800-56120800	Weak transcription	Fetal Brain Male	brain
14	chr12:56112800-56121000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr12:56113000-56116600	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr12:56113200-56117000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr12:56113200-56118000	Weak transcription	Ovary	ovary
18	chr12:56113200-56118600	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr12:56113200-56120000	Strong transcription	Brain Germinal Matrix	brain
20	chr12:56113200-56120800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr12:56113400-56117200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr12:56113600-56116000	Flanking Active TSS	Osteobl	bone
23	chr12:56113600-56116200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:56113600-56117400	Weak transcription	Fetal Heart	heart
25	chr12:56114000-56116200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr12:56114200-56117800	Strong transcription	Spleen	Spleen
27	chr12:56114200-56118600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
28	chr12:56114400-56116600	Weak transcription	GM12878-XiMat	blood
29	chr12:56114400-56117800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:56114400-56118000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:56114400-56118600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
32	chr12:56114400-56121000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:56114600-56116000	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr12:56114600-56116600	Weak transcription	Primary B cells from cord blood	blood
35	chr12:56114600-56116800	Weak transcription	Primary B cells from peripheral blood	blood
36	chr12:56114600-56118000	Weak transcription	Fetal Kidney	kidney
37	chr12:56114800-56116000	Enhancers	Stomach Mucosa	stomach
38	chr12:56114800-56116000	Active TSS	HSMMtube	muscle
39	chr12:56114800-56116200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:56114800-56118200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:56115000-56118600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:56115000-56118600	Weak transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:56115000-56120400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr12:56115200-56116000	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr12:56115200-56116000	Transcr. at gene 5' and 3'	HSMM	muscle
46	chr12:56115200-56116600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr12:56115200-56116600	Weak transcription	HepG2	liver
48	chr12:56115200-56117000	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr12:56115200-56117200	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr12:56115200-56118200	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links