Variant report

Variant	rs598144
Chromosome Location	chr12:50402567-50402568
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	chr12:50402547-50402645	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50401735..50404154-chr12:50407864..50410394,2	MCF-7	breast:
2	chr12:50400929..50402822-chr12:50417535..50420506,2	K562	blood:
3	chr12:50402351..50404081-chr12:50407613..50409709,2	K562	blood:
4	chr12:50402113..50404435-chr12:50411266..50413680,2	K562	blood:

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

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs192704	1.00[EUR][1000 genomes]
rs1967110	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
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]
rs602772	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs629874	0.96[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:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50369600-50418200	Weak transcription	Colonic Mucosa	Colon
2	chr12:50372400-50404800	Weak transcription	Spleen	Spleen
3	chr12:50377600-50403200	Weak transcription	Ovary	ovary
4	chr12:50377600-50405600	Strong transcription	Fetal Thymus	thymus
5	chr12:50378600-50412800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr12:50379000-50405800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr12:50379400-50405600	Strong transcription	Hela-S3	cervix
8	chr12:50379600-50403800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr12:50379800-50405400	Strong transcription	Dnd41	blood
10	chr12:50380200-50404800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr12:50380400-50410600	Weak transcription	Aorta	Aorta
12	chr12:50381600-50404000	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:50381800-50410400	Weak transcription	Small Intestine	intestine
14	chr12:50382000-50414800	Weak transcription	Psoas Muscle	Psoas
15	chr12:50383000-50418000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr12:50387400-50402600	Weak transcription	Left Ventricle	heart
17	chr12:50387600-50411800	Weak transcription	Lung	lung
18	chr12:50387800-50411600	Weak transcription	Esophagus	oesophagus
19	chr12:50388200-50418000	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr12:50391000-50418000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr12:50392000-50410400	Weak transcription	Adipose Nuclei	Adipose
22	chr12:50392800-50418200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr12:50393400-50411000	Weak transcription	Fetal Brain Female	brain
24	chr12:50393600-50407400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr12:50393600-50411000	Weak transcription	Liver	Liver
26	chr12:50395200-50404200	Weak transcription	Fetal Intestine Small	intestine
27	chr12:50395200-50408200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr12:50395400-50412200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr12:50397600-50412000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr12:50399200-50418200	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr12:50399400-50408200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr12:50399400-50412800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr12:50399600-50408800	Weak transcription	Placenta	Placenta
34	chr12:50399800-50410400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr12:50399800-50410800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:50399800-50417400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr12:50400200-50408000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr12:50400400-50407400	Weak transcription	Fetal Intestine Large	intestine
39	chr12:50400400-50411800	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr12:50400400-50418200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:50400600-50410400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr12:50400600-50418200	Weak transcription	Placenta Amnion	Placenta Amnion
43	chr12:50400800-50403200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr12:50400800-50403200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr12:50400800-50403600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr12:50400800-50407000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr12:50400800-50407200	Weak transcription	Fetal Muscle Trunk	muscle
48	chr12:50400800-50407400	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr12:50400800-50407400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:50400800-50407400	Weak transcription	Rectal Mucosa Donor 29	rectum

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