Variant report

Variant	rs2066571
Chromosome Location	chr13:50646218-50646219
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:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50645718..50648310-chr13:50652570..50656008,3	MCF-7	breast:
2	chr13:50638410..50642177-chr13:50643409..50648630,6	K562	blood:
3	chr13:50570406..50572751-chr13:50644478..50647028,2	MCF-7	breast:
4	chr13:50644274..50647771-chr13:50654406..50657878,4	MCF-7	breast:
5	chr13:50644302..50647195-chr13:50765968..50768337,2	K562	blood:
6	chr13:50645726..50647924-chr13:50649661..50651928,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DLEU1-2	chr13:50645106-50655642	NONHSAT033808

No data

Variant related genes	Relation type
ENSG00000176124	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000231607	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs11617754	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs2066549	0.86[CHB][hapmap]
rs2066557	0.86[CHB][hapmap];0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs2066575	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs2066585	0.86[CHB][hapmap]
rs2066591	0.86[CHB][hapmap]
rs2242482	0.86[CHB][hapmap];0.80[ASN][1000 genomes]
rs2472599	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2475837	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2687950	0.94[CHB][hapmap];0.82[JPT][hapmap]
rs2687951	0.86[CHB][hapmap]
rs2740524	0.86[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2740544	0.82[CHB][hapmap]
rs2740545	0.86[CHB][hapmap]
rs2760914	0.86[CHB][hapmap]
rs2803839	0.86[CHB][hapmap]
rs2812222	0.86[CHB][hapmap]
rs28798976	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3116591	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4548769	0.86[CHB][hapmap]
rs4942899	0.86[CHB][hapmap]
rs4942903	0.84[CHB][hapmap]
rs706610	0.82[CHB][hapmap]
rs73489861	0.82[ASN][1000 genomes]
rs73489862	0.82[ASN][1000 genomes]
rs790943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7986337	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs809845	0.82[CHB][hapmap]
rs9535407	0.86[CHB][hapmap];0.87[JPT][hapmap]
rs9562941	0.82[CHB][hapmap]
rs9568348	0.82[CHB][hapmap]
rs9568354	0.81[CHB][hapmap];0.86[JPT][hapmap]
rs9568357	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[YRI][hapmap];0.81[ASN][1000 genomes]
rs9568359	0.82[CHB][hapmap]
rs9568366	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9596219	0.86[CHB][hapmap]
rs9596220	0.86[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv1054415	chr13:50598121-50650938	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1202 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50578800-50654400	Weak transcription	Esophagus	oesophagus
2	chr13:50586800-50654200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:50590200-50653600	Weak transcription	Small Intestine	intestine
4	chr13:50595000-50654200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr13:50595800-50654400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:50598600-50650200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:50611800-50646400	Strong transcription	Fetal Thymus	thymus
8	chr13:50616000-50653600	Weak transcription	Fetal Kidney	kidney
9	chr13:50617400-50650000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:50617400-50654200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr13:50622600-50653400	Weak transcription	Fetal Brain Male	brain
12	chr13:50622800-50653400	Weak transcription	Rectal Smooth Muscle	rectum
13	chr13:50624400-50654200	Weak transcription	Pancreas	Pancrea
14	chr13:50625400-50654200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:50625600-50649000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:50626600-50654000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr13:50628400-50652400	Weak transcription	Psoas Muscle	Psoas
18	chr13:50630000-50651000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:50633000-50653600	Weak transcription	Fetal Stomach	stomach
20	chr13:50633400-50652200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr13:50638400-50653400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr13:50639800-50649000	Genic enhancers	Dnd41	blood
23	chr13:50640200-50650800	Weak transcription	Right Ventricle	heart
24	chr13:50640400-50649800	Weak transcription	Colon Smooth Muscle	Colon
25	chr13:50641200-50651600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr13:50641400-50654200	Weak transcription	Left Ventricle	heart
27	chr13:50641600-50650200	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr13:50641600-50651800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:50641600-50653600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr13:50641800-50654400	Weak transcription	Lung	lung
31	chr13:50642200-50647000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr13:50642200-50652400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr13:50642400-50652200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr13:50642600-50649600	Weak transcription	HepG2	liver
35	chr13:50642600-50651600	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr13:50642600-50653000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:50642600-50653600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr13:50642600-50654600	Weak transcription	Gastric	stomach
39	chr13:50643000-50652200	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr13:50643000-50652200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:50643000-50653200	Weak transcription	Duodenum Mucosa	Duodenum
42	chr13:50643200-50653400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr13:50643400-50647600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr13:50643400-50647600	Weak transcription	Hela-S3	cervix
45	chr13:50644000-50648600	Enhancers	Fetal Heart	heart
46	chr13:50644200-50651000	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr13:50644400-50646400	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr13:50644400-50649400	Enhancers	Primary B cells from cord blood	blood
49	chr13:50644800-50647800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr13:50645200-50646400	Enhancers	Brain Angular Gyrus	brain

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