Variant report

Variant	rs2388239
Chromosome Location	chr13:30499076-30499077
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:30498204..30500565-chr13:30503827..30506540,2	MCF-7	breast:
2	chr13:30419221..30420167-chr13:30498544..30499140,3	MCF-7	breast:
3	chr13:30498030..30500017-chr13:30505243..30508039,2	K562	blood:
4	chr13:30498435..30501654-chr13:30681390..30683059,3	MCF-7	breast:
5	chr13:30482306..30489173-chr13:30491895..30500288,16	MCF-7	breast:
6	chr13:30474561..30476361-chr13:30497151..30499609,2	MCF-7	breast:
7	chr13:30421079..30421752-chr13:30498389..30499250,2	MCF-7	breast:
8	chr13:30492675..30494704-chr13:30496918..30499167,3	MCF-7	breast:
9	chr13:30498140..30499691-chr13:30608886..30611160,2	MCF-7	breast:
10	chr13:30420595..30432624-chr13:30489594..30503683,39	MCF-7	breast:
11	chr13:30414305..30417482-chr13:30498003..30500774,5	MCF-7	breast:
12	chr13:30391873..30393700-chr13:30497127..30499566,2	MCF-7	breast:
13	chr13:30420962..30426189-chr13:30489163..30500098,34	MCF-7	breast:
14	chr13:30494996..30500904-chr13:30681667..30688775,12	MCF-7	breast:
15	chr13:30497791..30500360-chr13:30674614..30679278,4	MCF-7	breast:
16	chr13:30475291..30479868-chr13:30496674..30499474,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000122042	Chromatin interaction
ENSG00000224511	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1093631	0.92[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1325368	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs17074100	0.83[CHD][hapmap]
rs17074118	0.83[CHD][hapmap]
rs17631642	0.83[CHB][hapmap];0.85[JPT][hapmap];0.94[ASN][1000 genomes]
rs17688104	0.90[CHB][hapmap];0.86[JPT][hapmap];0.94[ASN][1000 genomes]
rs3843677	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs3843678	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73157197	0.80[ASN][1000 genomes]
rs7319246	0.92[ASN][1000 genomes]
rs7320271	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7320355	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7320728	0.92[ASN][1000 genomes]
rs7323424	0.88[CEU][hapmap]
rs74042894	0.92[ASN][1000 genomes]
rs7992473	0.92[CHB][hapmap];0.86[JPT][hapmap];0.92[ASN][1000 genomes]
rs7994222	0.80[ASN][1000 genomes]
rs927731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs927732	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs927733	0.92[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9508590	0.88[JPT][hapmap]
rs9508592	0.81[ASN][1000 genomes]
rs9508594	0.80[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	esv3520592	chr13:30243601-30648554	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	esv3520593	chr13:30243601-30648554	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv510598	chr13:30476386-30542798	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:30491600-30501000	Enhancers	Placenta Amnion	Placenta Amnion
2	chr13:30492400-30500600	Enhancers	HMEC	breast
3	chr13:30494200-30501400	Enhancers	Stomach Mucosa	stomach
4	chr13:30495600-30500400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr13:30496000-30500000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr13:30496000-30500200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:30496400-30499600	Enhancers	Pancreas	Pancrea
8	chr13:30496400-30499800	Enhancers	Right Ventricle	heart
9	chr13:30496400-30500000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr13:30496400-30500200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr13:30496400-30500200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr13:30496400-30500200	Enhancers	Fetal Muscle Leg	muscle
13	chr13:30496400-30500200	Enhancers	NHLF	lung
14	chr13:30496400-30500400	Enhancers	Placenta	Placenta
15	chr13:30496400-30500600	Enhancers	NHDF-Ad	bronchial
16	chr13:30496600-30499800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:30496600-30500000	Enhancers	Fetal Stomach	stomach
18	chr13:30496600-30500800	Enhancers	Liver	Liver
19	chr13:30496800-30499200	Enhancers	Thymus	Thymus
20	chr13:30496800-30499400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:30496800-30499600	Enhancers	Fetal Muscle Trunk	muscle
22	chr13:30496800-30499600	Enhancers	Left Ventricle	heart
23	chr13:30496800-30500200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr13:30496800-30500400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr13:30496800-30500800	Enhancers	Brain Hippocampus Middle	brain
26	chr13:30496800-30501000	Enhancers	Fetal Intestine Small	intestine
27	chr13:30497000-30500000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr13:30497000-30500000	Enhancers	Fetal Intestine Large	intestine
29	chr13:30497000-30500000	Enhancers	Fetal Thymus	thymus
30	chr13:30497000-30500000	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr13:30497000-30500800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr13:30497000-30501000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr13:30497200-30500000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr13:30497200-30500600	Enhancers	Primary T cells from cord blood	blood
35	chr13:30497200-30500600	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr13:30497200-30500800	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr13:30497200-30500800	Enhancers	Fetal Lung	lung
38	chr13:30497400-30499600	Enhancers	Esophagus	oesophagus
39	chr13:30497400-30500400	Enhancers	Fetal Heart	heart
40	chr13:30497400-30500600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr13:30497400-30500800	Enhancers	Cortex derived primary cultured neurospheres	brain
42	chr13:30497600-30499200	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr13:30497600-30499200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
44	chr13:30497600-30499400	Enhancers	Brain Substantia Nigra	brain
45	chr13:30497600-30499400	Enhancers	Colonic Mucosa	Colon
46	chr13:30497600-30499400	Enhancers	HUVEC	blood vessel
47	chr13:30497600-30499800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr13:30497600-30500000	Enhancers	Duodenum Mucosa	Duodenum
49	chr13:30497600-30500400	Enhancers	Brain Cingulate Gyrus	brain
50	chr13:30497600-30501000	Enhancers	Right Atrium	heart

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