Variant report

Variant	rs17123919
Chromosome Location	chr12:50142463-50142464
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:50142324-50142524	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr12:50141920-50142547	K562	blood:	n/a	n/a
3	POLR2A	chr12:50142134-50142541	HepG2	liver:	n/a	n/a
4	POLR2A	chr12:50142459-50142492	Hela-S3	cervix:	n/a	n/a
5	POLR2A	chr12:50142137-50142692	IMR90	lung:	n/a	n/a
6	POLR2A	chr12:50141974-50142547	GM12891	blood:	n/a	n/a
7	POLR2A	chr12:50141943-50142497	GM12891	blood:	n/a	n/a
8	POLR2A	chr12:50142024-50142601	GM12891	blood:	n/a	n/a
9	POLR2A	chr12:50142027-50142918	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:50142007-50143045	HepG2	liver:	n/a	n/a
11	POLR2A	chr12:50141915-50142605	GM12878	blood:	n/a	n/a
12	POLR2A	chr12:50142278-50142482	MCF-7	breast:	n/a	n/a
13	POLR2A	chr12:50142205-50142463	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr12:50142041-50142505	Hela-S3	cervix:	n/a	n/a
15	MAFK	chr12:50142155-50142463	IMR90	lung:	n/a	n/a
16	POLR2A	chr12:50141995-50142624	GM12892	blood:	n/a	n/a
17	POLR2A	chr12:50140846-50143188	A549	lung:	n/a	n/a
18	POLR2A	chr12:50142160-50143059	MCF10A-Er-Src	breast:	n/a	n/a
19	POLR2A	chr12:50141996-50142568	GM12892	blood:	n/a	n/a
20	POLR2A	chr12:50142064-50142495	K562	blood:	n/a	n/a
21	POLR2A	chr12:50141913-50142588	GM12892	blood:	n/a	n/a
22	POLR2A	chr12:50141924-50142623	GM12892	blood:	n/a	n/a
23	POLR2A	chr12:50141940-50142518	U87	brain:	n/a	n/a
24	POLR2A	chr12:50142223-50142533	H1-neurons	neurons:	n/a	n/a
25	POLR2A	chr12:50142104-50143146	K562	blood:	n/a	n/a
26	POLR2A	chr12:50142219-50142464	H1-neurons	neurons:	n/a	n/a
27	FOXA1	chr12:50142087-50142656	HepG2	liver:	n/a	chr12:50142524-50142539
28	POLR2A	chr12:50141069-50142595	GM12878	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:50141422..50142941-chr12:50168874..50170719,2	K562	blood:
2	chr12:50018757..50020272-chr12:50141476..50143680,2	K562	blood:
3	chr12:50142342..50144215-chr12:50231423..50233388,2	K562	blood:
4	chr12:50141474..50143579-chr12:50146279..50148343,2	MCF-7	breast:
5	chr12:50099618..50102364-chr12:50142236..50145462,3	K562	blood:
6	chr12:50141258..50143607-chr12:50154074..50155843,2	K562	blood:
7	chr12:50030639..50033047-chr12:50142456..50143972,2	MCF-7	breast:
8	chr12:50141439..50143610-chr12:50160538..50162943,2	MCF-7	breast:
9	chr12:50030562..50034220-chr12:50141044..50143029,3	K562	blood:

No data

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000161791	Chromatin interaction
ENSG00000110844	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs17123751	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs17123790	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs17123865	0.82[YRI][hapmap]
rs17123922	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17123943	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4144469	1.00[JPT][hapmap]
rs4569075	1.00[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50136600-50146400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:50136800-50144200	Enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr12:50136800-50146600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr12:50137000-50143800	Weak transcription	Colonic Mucosa	Colon
5	chr12:50137000-50146200	Weak transcription	HSMMtube	muscle
6	chr12:50137000-50147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr12:50137200-50146200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:50137400-50143200	Strong transcription	Fetal Thymus	thymus
10	chr12:50137400-50146400	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:50137400-50146400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr12:50137400-50146600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
14	chr12:50137600-50146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:50137800-50143800	Weak transcription	Fetal Stomach	stomach
16	chr12:50137800-50144200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr12:50137800-50146200	Weak transcription	Fetal Kidney	kidney
18	chr12:50138000-50143800	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr12:50138200-50146400	Weak transcription	Fetal Brain Female	brain
20	chr12:50138400-50143000	Weak transcription	Stomach Mucosa	stomach
21	chr12:50138400-50144000	Weak transcription	Fetal Lung	lung
22	chr12:50138600-50142600	Weak transcription	Pancreatic Islets	Pancreatic Islet
23	chr12:50138600-50142800	Weak transcription	NH-A	brain
24	chr12:50138600-50143400	Weak transcription	Fetal Muscle Trunk	muscle
25	chr12:50138600-50143800	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:50138600-50143800	Weak transcription	Small Intestine	intestine
27	chr12:50138600-50144000	Weak transcription	Esophagus	oesophagus
28	chr12:50138600-50144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr12:50138600-50146400	Weak transcription	Brain Germinal Matrix	brain
30	chr12:50138800-50143800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr12:50138800-50143800	Weak transcription	NHLF	lung
32	chr12:50138800-50144000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:50139000-50142800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr12:50139000-50143800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr12:50139000-50143800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr12:50139000-50143800	Weak transcription	Aorta	Aorta
37	chr12:50139000-50143800	Weak transcription	HUVEC	blood vessel
38	chr12:50139000-50144000	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:50139000-50146200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr12:50139000-50146600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr12:50139200-50142600	Weak transcription	Colon Smooth Muscle	Colon
42	chr12:50139200-50143400	Weak transcription	Primary monocytes fromperipheralblood	blood
43	chr12:50139200-50143800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
44	chr12:50139200-50143800	Weak transcription	Fetal Muscle Leg	muscle
45	chr12:50139600-50143800	Strong transcription	Primary B cells from cord blood	blood
46	chr12:50140200-50142800	Enhancers	Skeletal Muscle Female	skeletal muscle
47	chr12:50140200-50143000	Strong transcription	Placenta	Placenta
48	chr12:50140400-50143400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr12:50140600-50143400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
50	chr12:50140600-50144000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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