Variant report

Variant	rs2238144
Chromosome Location	chr12:48139351-48139352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:48138236-48139493	ECC-1	luminal epithelium:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:48136388..48139799-chr12:48164464..48168424,4	K562	blood:
2	chr12:48138966..48141373-chr12:48164046..48166079,2	K562	blood:
3	chr12:48135601..48138663-chr12:48139025..48142154,4	K562	blood:
4	chr12:48138994..48139580-chr12:48153253..48153916,2	MCF-7	breast:
5	chr12:48139218..48143283-chr12:48146093..48149337,5	K562	blood:
6	chr12:48138983..48141594-chr12:48155266..48156809,2	K562	blood:
7	chr12:48131407..48141823-chr12:48163910..48172152,16	MCF-7	breast:
8	chr12:48136735..48141051-chr12:48142699..48146079,6	K562	blood:

No data

Variant related genes	Relation type
RAPGEF3	TF binding region
ENSG00000211584	Chromatin interaction
ENSG00000079337	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10875683	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs11168194	0.81[JPT][hapmap]
rs11168212	0.86[ASN][1000 genomes]
rs11168219	0.89[ASN][1000 genomes]
rs11168220	0.87[ASN][1000 genomes]
rs11830795	1.00[JPT][hapmap]
rs11834770	1.00[JPT][hapmap]
rs1235152	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12812960	0.82[ASN][1000 genomes]
rs12819759	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs12828238	0.89[ASN][1000 genomes]
rs2074531	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs2074532	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs2239188	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs2283345	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs2285830	1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs3764015	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs3764020	0.93[CEU][hapmap];1.00[JPT][hapmap]
rs4505143	0.81[ASN][1000 genomes]
rs6580635	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs6580636	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs7133585	0.86[ASN][1000 genomes]
rs726588	0.81[ASN][1000 genomes]
rs7306556	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs757284	0.87[CEU][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs7967336	0.94[CEU][hapmap];1.00[JPT][hapmap]
rs7967546	0.93[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1813565	chr12:48097697-48177858	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv470289	chr12:48110551-48180508	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer 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	75 gene(s)	inside rSNPs	diseases
4	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
6	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
7	nsv527470	chr12:48119955-48190166	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
8	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48129000-48147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:48129400-48146600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr12:48130000-48146000	Weak transcription	Small Intestine	intestine
4	chr12:48131000-48143000	Weak transcription	Aorta	Aorta
5	chr12:48131200-48141600	Weak transcription	Fetal Kidney	kidney
6	chr12:48131200-48145600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr12:48131800-48141000	Weak transcription	Gastric	stomach
8	chr12:48132400-48146600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr12:48134800-48147000	Weak transcription	Psoas Muscle	Psoas
10	chr12:48135000-48145400	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:48135200-48140200	Weak transcription	Fetal Intestine Small	intestine
12	chr12:48135400-48139800	Weak transcription	Ovary	ovary
13	chr12:48135400-48147000	Weak transcription	Colonic Mucosa	Colon
14	chr12:48135400-48147000	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr12:48135600-48139600	Weak transcription	Lung	lung
16	chr12:48135600-48140400	Weak transcription	Esophagus	oesophagus
17	chr12:48135600-48148000	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:48135800-48139800	Weak transcription	Spleen	Spleen
19	chr12:48135800-48140200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:48135800-48140600	Weak transcription	HUVEC	blood vessel
21	chr12:48135800-48145400	Weak transcription	NHDF-Ad	bronchial
22	chr12:48136000-48139400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr12:48136000-48139600	Weak transcription	Primary B cells from cord blood	blood
24	chr12:48136000-48146200	Weak transcription	Osteobl	bone
25	chr12:48136000-48147400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr12:48136400-48140400	Weak transcription	Placenta	Placenta
27	chr12:48136600-48139400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:48136600-48140400	Weak transcription	Stomach Mucosa	stomach
29	chr12:48136600-48142400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:48137000-48139800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr12:48137200-48139800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:48137400-48139800	Enhancers	Brain Hippocampus Middle	brain
33	chr12:48137400-48142000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr12:48137800-48139400	Enhancers	Brain Cingulate Gyrus	brain
35	chr12:48137800-48139600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr12:48137800-48140000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr12:48137800-48145200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr12:48138000-48139800	Weak transcription	Adipose Nuclei	Adipose
39	chr12:48138000-48140600	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:48138000-48141000	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr12:48138000-48144200	Weak transcription	Pancreas	Pancrea
42	chr12:48138000-48148000	Weak transcription	Liver	Liver
43	chr12:48138200-48140000	Enhancers	Brain Germinal Matrix	brain
44	chr12:48138400-48140000	Enhancers	Brain Substantia Nigra	brain
45	chr12:48138400-48140200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:48138400-48146600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:48138600-48139400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:48138600-48139600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr12:48138600-48139800	Enhancers	Brain Angular Gyrus	brain
50	chr12:48138600-48140200	Enhancers	Fetal Heart	heart

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