Variant report

Variant	rs13146448
Chromosome Location	chr4:144259648-144259649
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	ARID3A	chr4:144258865-144259787	HepG2	liver:	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	chr4:144257935..144259880-chr4:144296110..144298167,2	MCF-7	breast:
4	chr4:144256474..144260869-chr4:144433151..144436933,4	K562	blood:

Variant related genes	Relation type
ENSG00000178972	TF binding region
MIR3139	TF binding region
ENSG00000245112	Chromatin interaction
ENSG00000109458	Chromatin interaction
ENSG00000250326	Chromatin interaction
ENSG00000153147	Chromatin interaction
ENSG00000170185	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10025700	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11941986	0.88[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12331265	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13105156	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13133540	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	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28377860	0.81[AFR][1000 genomes]
rs28397211	0.81[AMR][1000 genomes]
rs28408110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28676298	0.92[AFR][1000 genomes]
rs28846534	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs300950	1.00[CHB][hapmap]
rs300954	1.00[CHB][hapmap]
rs300955	1.00[CHB][hapmap]
rs34420992	0.85[AMR][1000 genomes]
rs6826079	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9990577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9993972	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3406126	chr4:144256927-144259675	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:144256600-144259800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr4:144256600-144259800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr4:144256600-144259800	Active TSS	Colon Smooth Muscle	Colon
4	chr4:144256600-144259800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
5	chr4:144256600-144259800	Active TSS	Fetal Intestine Large	intestine
6	chr4:144256600-144259800	Active TSS	Ovary	ovary
7	chr4:144256600-144259800	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr4:144256600-144259800	Active TSS	NHDF-Ad	bronchial
9	chr4:144256600-144260000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr4:144256600-144260200	Active TSS	Duodenum Smooth Muscle	Duodenum
11	chr4:144256600-144260200	Active TSS	NHLF	lung
12	chr4:144256600-144260400	Active TSS	Duodenum Mucosa	Duodenum
13	chr4:144256600-144260600	Active TSS	Brain Hippocampus Middle	brain
14	chr4:144256600-144260600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
15	chr4:144256600-144260800	Active TSS	Brain Anterior Caudate	brain
16	chr4:144256600-144260800	Active TSS	Right Ventricle	heart
17	chr4:144256600-144261200	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr4:144256800-144259800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr4:144256800-144259800	Active TSS	Brain Angular Gyrus	brain
20	chr4:144256800-144259800	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr4:144256800-144259800	Active TSS	Placenta Amnion	Placenta Amnion
22	chr4:144256800-144260800	Active TSS	Brain Substantia Nigra	brain
23	chr4:144256800-144261000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr4:144256800-144261600	Active TSS	Aorta	Aorta
25	chr4:144256800-144262000	Active TSS	Brain Inferior Temporal Lobe	brain
26	chr4:144257000-144259800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr4:144257000-144259800	Active TSS	Fetal Intestine Small	intestine
28	chr4:144257000-144260000	Active TSS	Fetal Stomach	stomach
29	chr4:144257000-144260600	Active TSS	Brain Cingulate Gyrus	brain
30	chr4:144257400-144260600	Active TSS	Colonic Mucosa	Colon
31	chr4:144258400-144259800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
32	chr4:144258400-144260000	Active TSS	Right Atrium	heart
33	chr4:144258600-144259800	Flanking Active TSS	Primary B cells from cord blood	blood
34	chr4:144258600-144259800	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr4:144259000-144259800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr4:144259000-144260000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr4:144259200-144259800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
38	chr4:144259200-144259800	Enhancers	Fetal Brain Male	brain
39	chr4:144259200-144259800	Active TSS	Fetal Brain Female	brain
40	chr4:144259200-144259800	Active TSS	Fetal Muscle Leg	muscle
41	chr4:144259200-144259800	Flanking Active TSS	HepG2	liver
42	chr4:144259200-144262600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr4:144259200-144262600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr4:144259200-144262600	Weak transcription	Gastric	stomach
45	chr4:144259200-144262600	Weak transcription	Spleen	Spleen
46	chr4:144259200-144264000	Weak transcription	Small Intestine	intestine
47	chr4:144259200-144272400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr4:144259400-144259800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr4:144259400-144259800	Enhancers	Primary monocytes fromperipheralblood	blood
50	chr4:144259400-144259800	Enhancers	Primary neutrophils fromperipheralblood	blood

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