Variant report

Variant	rs3742096
Chromosome Location	chr13:50354728-50354729
allele	C/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:7)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50353952..50356065-chr13:50366891..50368396,2	K562	blood:
2	chr13:50353952..50356352-chr13:50366009..50368396,2	K562	blood:
3	chr13:50352653..50354938-chr13:50357340..50359158,2	MCF-7	breast:
4	chr13:50351267..50358317-chr13:50361760..50368621,11	MCF-7	breast:
5	chr13:50244133..50245695-chr13:50352710..50354837,2	MCF-7	breast:
6	chr13:50354262..50357450-chr13:50365165..50368235,4	MCF-7	breast:
7	chr13:50343988..50346114-chr13:50354388..50356703,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EBPL-2	chr13:50354651-50354767	ENSG00000224798.1
2	lnc-EBPL-2	chr13:50354633-50354782	l_841_chr13:50354493-50361781_adrenal

No data

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1008939	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12019576	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1407439	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs35526541	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs58303577	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961485	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61961487	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7324563	0.82[EUR][1000 genomes]
rs7328465	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7332209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs748678	0.95[CEU][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs7982919	0.95[CEU][hapmap];1.00[CHB][hapmap]
rs7983049	0.94[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7996689	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7999786	1.00[JPT][hapmap]
rs9316478	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9526603	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9526606	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9535318	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535320	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535323	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535325	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535327	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535331	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9535346	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535351	1.00[CHB][hapmap]
rs9535360	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9535361	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9535362	0.81[EUR][1000 genomes]
rs9535366	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs957474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1038	chr13:50324773-50359990	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3742096	ITM2B	cis	parietal	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
2	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
4	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
5	chr13:50336800-50364600	Weak transcription	NHLF	lung
6	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr13:50344000-50355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:50349600-50357600	Weak transcription	Gastric	stomach
12	chr13:50349600-50357600	Weak transcription	Left Ventricle	heart
13	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:50349600-50365400	Weak transcription	Lung	lung
15	chr13:50349800-50355200	Weak transcription	Fetal Heart	heart
16	chr13:50350400-50356200	Weak transcription	Ovary	ovary
17	chr13:50350600-50358600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr13:50351200-50364200	Weak transcription	HSMM	muscle
19	chr13:50351200-50364600	Weak transcription	HSMMtube	muscle
20	chr13:50351400-50362600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr13:50351400-50363000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
22	chr13:50351600-50355600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr13:50351600-50359200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:50351600-50359200	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:50351600-50360800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr13:50351600-50363800	Weak transcription	HUES6 Cell Line	embryonic stem cell
27	chr13:50351800-50359400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr13:50351800-50363800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr13:50351800-50364000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr13:50352000-50356000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr13:50352000-50365200	Weak transcription	Fetal Thymus	thymus
32	chr13:50352400-50364400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr13:50352600-50355200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr13:50352600-50355600	Weak transcription	Pancreatic Islets	Pancreatic Islet
35	chr13:50352600-50355800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr13:50352600-50358200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr13:50352600-50363800	Weak transcription	Pancreas	Pancrea
38	chr13:50352600-50363800	Weak transcription	Thymus	Thymus
39	chr13:50352600-50364800	Weak transcription	A549	lung
40	chr13:50353000-50356000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr13:50353000-50358000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr13:50353000-50359200	Weak transcription	Liver	Liver
43	chr13:50353000-50359800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
44	chr13:50353000-50360400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr13:50353000-50363800	Weak transcription	Primary T cells fromperipheralblood	blood
46	chr13:50353000-50363800	Weak transcription	Small Intestine	intestine
47	chr13:50353200-50355600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr13:50353200-50360800	Weak transcription	Primary T cells from cord blood	blood
49	chr13:50353600-50357400	Weak transcription	Fetal Muscle Leg	muscle
50	chr13:50353800-50354800	Enhancers	HUES64 Cell Line	embryonic stem cell

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