Variant report

Variant	rs17123922
Chromosome Location	chr12:50143908-50143909
allele	A/G
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	POLR2A	chr12:50143825-50144934	GM12892	blood:	n/a	n/a
2	RUNX3	chr12:50143729-50144080	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:50143747-50144666	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr12:50143782-50144612	GM12878	blood:	n/a	n/a
5	RCOR1	chr12:50143908-50144019	GM12878	blood:	n/a	n/a
6	CHD2	chr12:50143858-50144014	GM12878	blood:	n/a	n/a
7	POLR2A	chr12:50143808-50144649	H1-hESC	embryonic stem cell:	n/a	n/a
8	NFATC1	chr12:50143729-50144393	GM12878	blood:	n/a	n/a
9	POLR2A	chr12:50143829-50144722	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:50143825-50144952	Hela-S3	cervix:	n/a	n/a
11	RUNX3	chr12:50143407-50144603	GM12878	blood:	n/a	n/a
12	CUX1	chr12:50143853-50144423	GM12878	blood:	n/a	n/a
13	POLR2A	chr12:50143843-50144082	H1-hESC	embryonic stem cell:	n/a	n/a
14	FOXM1	chr12:50143771-50144186	GM12878	blood:	n/a	n/a
15	POLR2A	chr12:50143479-50145095	K562	blood:	n/a	n/a
16	POLR2A	chr12:50143895-50144882	GM12878	blood:	n/a	n/a
17	TBL1XR1	chr12:50143714-50144781	GM12878	blood:	n/a	n/a
18	CHD1	chr12:50143688-50144017	GM12878	blood:	n/a	n/a
19	EBF1	chr12:50143802-50144385	GM12878	blood:	n/a	chr12:50143944-50143955
20	POLR2A	chr12:50143785-50144948	HepG2	liver:	n/a	n/a
21	TBP	chr12:50143802-50144591	GM12878	blood:	n/a	n/a
22	POLR2A	chr12:50143526-50145034	A549	lung:	n/a	n/a
23	POLR2A	chr12:50143780-50144611	GM12891	blood:	n/a	n/a
24	POLR2A	chr12:50143854-50144504	Hela-S3	cervix:	n/a	n/a
25	NFIC	chr12:50143612-50144609	GM12878	blood:	n/a	n/a
26	EBF1	chr12:50143742-50144677	GM12878	blood:	n/a	chr12:50143944-50143955
27	POLR2A	chr12:50143326-50145014	GM12892	blood:	n/a	n/a
28	WRNIP1	chr12:50143846-50144713	GM12878	blood:	n/a	n/a
29	POLR2A	chr12:50143841-50144592	GM12891	blood:	n/a	n/a
30	RFX5	chr12:50143908-50144019	GM12878	blood:	n/a	n/a
31	POLR2A	chr12:50143788-50144782	GM12891	blood:	n/a	n/a
32	POLR2A	chr12:50143776-50144956	K562	blood:	n/a	n/a
33	MAZ	chr12:50143852-50144399	GM12878	blood:	n/a	n/a
34	EP300	chr12:50143736-50144613	GM12878	blood:	n/a	chr12:50143749-50143763 chr12:50144363-50144377
35	POLR2A	chr12:50143526-50145493	K562	blood:	n/a	n/a
36	POLR2A	chr12:50143895-50144552	IMR90	lung:	n/a	n/a
37	JUN	chr12:50143426-50145488	K562	blood:	n/a	chr12:50145327-50145336 chr12:50144399-50144407 chr12:50144400-50144411
38	POLR2A	chr12:50143802-50144735	GM12892	blood:	n/a	n/a
39	EP300	chr12:50143724-50144380	GM12878	blood:	n/a	chr12:50143749-50143763 chr12:50144363-50144377
40	IKZF1	chr12:50143840-50144586	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50142342..50144215-chr12:50231423..50233388,2	K562	blood:
2	chr12:50030201..50031969-chr12:50143354..50146117,2	K562	blood:
3	chr12:50142752..50145043-chr12:50235081..50237094,3	K562	blood:
4	chr12:50099618..50102364-chr12:50142236..50145462,3	K562	blood:
5	chr12:50030639..50033047-chr12:50142456..50143972,2	MCF-7	breast:

Variant related genes	Relation type
TMBIM6	TF binding region
ENSG00000110844	Chromatin interaction
ENSG00000161791	Chromatin interaction
ENSG00000139644	Chromatin interaction
ENSG00000186666	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]
rs17123790	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes]
rs17123865	1.00[YRI][hapmap]
rs17123919	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];1.00[YRI][hapmap];1.00[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];1.00[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:127 , 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	chr12:50137000-50146200	Weak transcription	HSMMtube	muscle
5	chr12:50137000-50147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr12:50137200-50146200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:50137200-50152000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:50137400-50146400	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr12:50137400-50146400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:50137400-50146600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr12:50137400-50150800	Weak transcription	Fetal Brain Male	brain
12	chr12:50137600-50146200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr12:50137800-50144200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:50137800-50146200	Weak transcription	Fetal Kidney	kidney
15	chr12:50138200-50146400	Weak transcription	Fetal Brain Female	brain
16	chr12:50138400-50144000	Weak transcription	Fetal Lung	lung
17	chr12:50138600-50144000	Weak transcription	Esophagus	oesophagus
18	chr12:50138600-50144200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr12:50138600-50146400	Weak transcription	Brain Germinal Matrix	brain
20	chr12:50138800-50144000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr12:50139000-50144000	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr12:50139000-50146200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr12:50139000-50146600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr12:50140600-50144000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
25	chr12:50140800-50144600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:50141000-50144000	Strong transcription	A549	lung
27	chr12:50141000-50146200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr12:50141400-50144000	Genic enhancers	NHEK	skin
29	chr12:50141400-50144200	Genic enhancers	Fetal Intestine Small	intestine
30	chr12:50141400-50146800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr12:50141600-50144000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr12:50141800-50144000	Enhancers	Liver	Liver
33	chr12:50141800-50144600	Enhancers	Right Atrium	heart
34	chr12:50142000-50144000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:50142000-50144000	Flanking Active TSS	GM12878-XiMat	blood
36	chr12:50142000-50145000	Enhancers	ES-I3 Cell Line	embryonic stem cell
37	chr12:50142000-50145000	Genic enhancers	Dnd41	blood
38	chr12:50142200-50144800	Genic enhancers	Primary T cells from cord blood	blood
39	chr12:50142200-50148200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr12:50142400-50144000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr12:50142400-50144200	Weak transcription	Ovary	ovary
42	chr12:50142600-50144000	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:50142600-50144000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:50142600-50144000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:50142600-50144000	Weak transcription	Adipose Nuclei	Adipose
46	chr12:50142600-50144000	Weak transcription	NHDF-Ad	bronchial
47	chr12:50142600-50144200	Weak transcription	Brain Anterior Caudate	brain
48	chr12:50142600-50144200	Enhancers	Thymus	Thymus
49	chr12:50142600-50144600	Enhancers	Pancreatic Islets	Pancreatic Islet
50	chr12:50142800-50144000	Weak transcription	Brain Substantia Nigra	brain

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