Variant report

Variant	rs13133540
Chromosome Location	chr4:144260239-144260240
allele	C/T
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	chr4:144260042-144260240	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:144104818..144107585-chr4:144256509..144260468,4	MCF-7	breast:
2	chr4:144106120..144108984-chr4:144259325..144260882,2	K562	blood:
3	chr4:144256474..144260869-chr4:144433151..144436933,4	K562	blood:

Variant related genes	Relation type
ENSG00000178972	TF binding region
MIR3139	TF binding region
ENSG00000153147	Chromatin interaction
ENSG00000170185	Chromatin interaction
ENSG00000250326	Chromatin interaction
ENSG00000245112	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10025700	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941986	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12331265	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13105156	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13146448	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2323079	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28397211	0.81[EUR][1000 genomes]
rs28408110	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676298	0.89[AFR][1000 genomes]
rs28846534	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300950	1.00[CHB][hapmap]
rs300954	1.00[CHB][hapmap]
rs300955	1.00[CHB][hapmap]
rs34420992	0.81[AMR][1000 genomes]
rs6826079	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990577	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993972	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][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	nsv1033902	chr4:144114413-144285772	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1026110	chr4:144239825-144292148	Enhancers Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144256600-144260400	Active TSS	Duodenum Mucosa	Duodenum
2	chr4:144256600-144260600	Active TSS	Brain Hippocampus Middle	brain
3	chr4:144256600-144260600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr4:144256600-144260800	Active TSS	Brain Anterior Caudate	brain
5	chr4:144256600-144260800	Active TSS	Right Ventricle	heart
6	chr4:144256600-144261200	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr4:144256800-144260800	Active TSS	Brain Substantia Nigra	brain
8	chr4:144256800-144261000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:144256800-144261600	Active TSS	Aorta	Aorta
10	chr4:144256800-144262000	Active TSS	Brain Inferior Temporal Lobe	brain
11	chr4:144257000-144260600	Active TSS	Brain Cingulate Gyrus	brain
12	chr4:144257400-144260600	Active TSS	Colonic Mucosa	Colon
13	chr4:144259200-144262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:144259200-144262600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr4:144259200-144262600	Weak transcription	Gastric	stomach
16	chr4:144259200-144262600	Weak transcription	Spleen	Spleen
17	chr4:144259200-144264000	Weak transcription	Small Intestine	intestine
18	chr4:144259200-144272400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:144259400-144260400	Weak transcription	Pancreas	Pancrea
20	chr4:144259400-144260400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:144259400-144262600	Weak transcription	Esophagus	oesophagus
22	chr4:144259400-144262600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr4:144259400-144262600	Weak transcription	Lung	lung
24	chr4:144259400-144265400	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr4:144259400-144268600	Weak transcription	Primary B cells from peripheral blood	blood
26	chr4:144259400-144272000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr4:144259400-144272600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr4:144259600-144260400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:144259600-144260400	Weak transcription	Placenta	Placenta
30	chr4:144259600-144260400	Weak transcription	Left Ventricle	heart
31	chr4:144259600-144260400	Weak transcription	Psoas Muscle	Psoas
32	chr4:144259600-144260600	Flanking Active TSS	Fetal Heart	heart
33	chr4:144259600-144261000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr4:144259600-144261200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr4:144259600-144261400	Enhancers	Liver	Liver
36	chr4:144259600-144262600	Weak transcription	Fetal Thymus	thymus
37	chr4:144259600-144264200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr4:144259600-144264200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
39	chr4:144259600-144264600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr4:144259600-144265000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr4:144259600-144276200	Weak transcription	Fetal Kidney	kidney
42	chr4:144259800-144260400	Flanking Active TSS	Brain Angular Gyrus	brain
43	chr4:144259800-144260400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr4:144259800-144260400	Weak transcription	Ovary	ovary
45	chr4:144259800-144260600	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr4:144259800-144260600	Weak transcription	Fetal Muscle Leg	muscle
47	chr4:144259800-144260800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr4:144259800-144260800	Weak transcription	K562	blood
49	chr4:144259800-144261000	Enhancers	Primary B cells from cord blood	blood
50	chr4:144259800-144261000	Active TSS	Rectal Smooth Muscle	rectum

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