Variant report

Variant	rs602772
Chromosome Location	chr12:50398913-50398914
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	GATA3	chr12:50398786-50399175	SH-SY5Y	brain:	n/a	chr12:50398967-50398983
2	MXI1	chr12:50397800-50401671	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr12:50398812-50399438	SK-N-SH	brain:	n/a	n/a
4	EP300	chr12:50398862-50399294	SK-N-SH_RA	brain:	n/a	n/a
5	EP300	chr12:50398843-50399319	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50398309..50400753-chr12:50413166..50414946,2	K562	blood:
2	chr12:50386020..50388679-chr12:50398398..50401529,3	MCF-7	breast:
3	chr12:50398171..50399787-chr12:50403220..50405430,2	K562	blood:
4	chr12:50395341..50399448-chr12:50410625..50413867,3	K562	blood:

Variant related genes	Relation type
RACGAP1	TF binding region
ENSG00000161800	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs192704	1.00[EUR][1000 genomes]
rs1967110	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2232208	1.00[MEX][hapmap]
rs2603113	1.00[MEX][hapmap]
rs296751	1.00[EUR][1000 genomes]
rs296752	1.00[EUR][1000 genomes]
rs370774	1.00[EUR][1000 genomes]
rs438304	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs598144	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs629874	1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
3	nsv522972	chr12:50196394-50410831	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS 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 miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
5	nsv832407	chr12:50243268-50412236	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv558835	chr12:50275137-50433234	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv469374	chr12:50349765-50467769	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv469375	chr12:50349765-50467769	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv558837	chr12:50349765-50467769	Bivalent/Poised TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
10	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50367400-50401200	Weak transcription	Gastric	stomach
2	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
3	chr12:50372400-50404800	Weak transcription	Spleen	Spleen
4	chr12:50377600-50403200	Weak transcription	Ovary	ovary
5	chr12:50377600-50405600	Strong transcription	Fetal Thymus	thymus
6	chr12:50377800-50399800	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:50377800-50400800	Strong transcription	Thymus	Thymus
8	chr12:50378000-50399000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:50378200-50399200	Weak transcription	Fetal Brain Male	brain
10	chr12:50378200-50400000	Weak transcription	HSMMtube	muscle
11	chr12:50378600-50400600	Strong transcription	A549	lung
12	chr12:50378600-50412800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr12:50378800-50401400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:50379000-50405800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr12:50379200-50401400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr12:50379400-50401400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr12:50379400-50405600	Strong transcription	Hela-S3	cervix
18	chr12:50379600-50400200	Strong transcription	GM12878-XiMat	blood
19	chr12:50379600-50403800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr12:50379800-50400600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:50379800-50401200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr12:50379800-50401600	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr12:50379800-50405400	Strong transcription	Dnd41	blood
24	chr12:50380200-50400800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr12:50380200-50404800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:50380400-50410600	Weak transcription	Aorta	Aorta
27	chr12:50381200-50401400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
28	chr12:50381400-50401600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr12:50381600-50402000	Strong transcription	HUES48 Cell Line	embryonic stem cell
30	chr12:50381600-50404000	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr12:50381800-50410400	Weak transcription	Small Intestine	intestine
32	chr12:50382000-50400800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:50382000-50414800	Weak transcription	Psoas Muscle	Psoas
34	chr12:50382400-50400800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
35	chr12:50383000-50418000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr12:50384800-50400800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:50385800-50401000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr12:50386000-50400800	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr12:50386000-50401200	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr12:50386400-50401800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
41	chr12:50386800-50400600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr12:50387400-50399200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr12:50387400-50402600	Weak transcription	Left Ventricle	heart
44	chr12:50387600-50411800	Weak transcription	Lung	lung
45	chr12:50387800-50411600	Weak transcription	Esophagus	oesophagus
46	chr12:50388200-50418000	Weak transcription	Rectal Mucosa Donor 31	rectum
47	chr12:50390400-50401200	Strong transcription	Primary hematopoietic stem cells	blood
48	chr12:50391000-50418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
49	chr12:50391600-50400400	Strong transcription	HMEC	breast
50	chr12:50391600-50400600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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