Variant report

Variant	rs1539414
Chromosome Location	chr1:197743506-197743507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:197740776..197744504-chr1:197869951..197872253,3	K562	blood:
2	chr1:197742347..197745266-chr1:197870109..197873225,5	MCF-7	breast:
3	chr1:197743169..197745443-chr1:197870802..197873145,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203724	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11583319	1.00[CHB][hapmap];0.89[CHD][hapmap];0.88[GIH][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs11588864	0.81[ASN][1000 genomes]
rs12092948	0.81[ASN][1000 genomes]
rs12117045	0.88[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs12121863	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12123169	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12134279	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12141028	1.00[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap]
rs12354257	1.00[CHB][hapmap];0.93[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs1573100	0.82[ASN][1000 genomes]
rs16841904	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs16841912	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17641524	0.94[CEU][hapmap];0.91[GIH][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes]
rs1775452	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1998598	0.89[ASN][1000 genomes]
rs2477059	0.82[ASN][1000 genomes]
rs2477077	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[TSI][hapmap]
rs2488389	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap]
rs2488391	0.81[ASN][1000 genomes]
rs2488393	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2488397	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2488398	0.93[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2488401	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3900909	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9427672	0.89[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	nsv427908	chr1:197611569-197767362	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	esv3442149	chr1:197743379-197745627	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1539414	DENND1B	cis	parietal	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:197702800-197743800	Weak transcription	Esophagus	oesophagus
2	chr1:197714400-197743800	Weak transcription	Spleen	Spleen
3	chr1:197714600-197743600	Weak transcription	Ovary	ovary
4	chr1:197719200-197743800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:197735200-197743800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:197737400-197743600	Weak transcription	Fetal Muscle Trunk	muscle
7	chr1:197739000-197743600	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr1:197740400-197743800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:197741800-197743600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr1:197742000-197743600	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr1:197742000-197743800	Weak transcription	Left Ventricle	heart
12	chr1:197742000-197743800	Weak transcription	Lung	lung
13	chr1:197742000-197743800	Weak transcription	Pancreas	Pancrea
14	chr1:197742200-197743600	Enhancers	Primary neutrophils fromperipheralblood	blood
15	chr1:197742200-197743800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
16	chr1:197742200-197743800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr1:197742400-197743600	Flanking Active TSS	Primary T cells from cord blood	blood
18	chr1:197742400-197743800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
19	chr1:197742400-197744000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:197742400-197744000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr1:197742400-197744000	Active TSS	Right Atrium	heart
22	chr1:197742400-197744800	Active TSS	Colonic Mucosa	Colon
23	chr1:197742400-197745000	Active TSS	Brain Anterior Caudate	brain
24	chr1:197742400-197745000	Active TSS	Duodenum Smooth Muscle	Duodenum
25	chr1:197742600-197743600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr1:197742600-197743800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr1:197742600-197743800	Weak transcription	Gastric	stomach
28	chr1:197742600-197743800	Weak transcription	Small Intestine	intestine
29	chr1:197742600-197743800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
30	chr1:197742600-197743800	Flanking Active TSS	Osteobl	bone
31	chr1:197742600-197744600	Active TSS	Thymus	Thymus
32	chr1:197742600-197744800	Active TSS	K562	blood
33	chr1:197742600-197744800	Active TSS	NHLF	lung
34	chr1:197742600-197745000	Active TSS	Aorta	Aorta
35	chr1:197742800-197743600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
36	chr1:197742800-197743600	Weak transcription	Stomach Mucosa	stomach
37	chr1:197742800-197743800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
38	chr1:197742800-197743800	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
39	chr1:197742800-197743800	Flanking Active TSS	Rectal Smooth Muscle	rectum
40	chr1:197742800-197744000	Flanking Active TSS	HUVEC	blood vessel
41	chr1:197742800-197744600	Active TSS	Primary hematopoietic stem cells short term culture	blood
42	chr1:197742800-197744600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr1:197742800-197744600	Active TSS	Fetal Thymus	thymus
44	chr1:197742800-197744600	Active TSS	GM12878-XiMat	blood
45	chr1:197742800-197744800	Active TSS	Duodenum Mucosa	Duodenum
46	chr1:197742800-197744800	Active TSS	Fetal Stomach	stomach
47	chr1:197742800-197744800	Active TSS	Rectal Mucosa Donor 29	rectum
48	chr1:197743000-197743600	Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr1:197743000-197743800	Flanking Active TSS	Primary B cells from cord blood	blood
50	chr1:197743000-197743800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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