Variant report

Variant	rs13402735
Chromosome Location	chr2:40357672-40357673
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10167639	0.89[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10177338	0.94[CEU][hapmap];0.90[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10183046	0.89[CEU][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674059	0.90[ASW][hapmap];0.88[CEU][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11684633	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13385233	0.90[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13389504	0.80[GIH][hapmap];0.84[MEX][hapmap]
rs13405865	0.89[CEU][hapmap];0.80[JPT][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13409965	0.81[ASW][hapmap];0.86[TSI][hapmap]
rs13426771	0.89[ASN][1000 genomes]
rs13433080	0.94[CEU][hapmap];0.82[CHB][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1861427	0.86[TSI][hapmap]
rs2006286	0.93[ASN][1000 genomes]
rs2006287	0.93[ASN][1000 genomes]
rs2058693	0.85[CHB][hapmap];0.93[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2110921	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs409620	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4140823	0.90[ASW][hapmap];0.88[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4952469	0.85[ASN][1000 genomes]
rs5541	0.84[MEX][hapmap]
rs5543	0.94[CEU][hapmap];0.80[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.82[AMR][1000 genomes]
rs5546	0.89[MEX][hapmap]
rs6544310	0.80[EUR][1000 genomes]
rs6544311	0.90[CHB][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs67997642	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs72935262	0.92[ASN][1000 genomes]
rs765554	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs765555	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs918046	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833892	chr2:40188785-40363480	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv873902	chr2:40231282-40466268	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv1004092	chr2:40264608-40451701	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv1000572	chr2:40271958-40458911	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv535654	chr2:40271958-40458911	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv581502	chr2:40273903-40459645	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv873903	chr2:40285145-40382712	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv873904	chr2:40292289-40466268	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv873905	chr2:40341847-40364895	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
11	nsv873906	chr2:40341847-40385045	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv873907	chr2:40349094-40381369	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv1005758	chr2:40349403-40381369	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv873908	chr2:40351453-40371095	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13402735	CYP1B1	cis	cerebellum	SCAN
rs13402735	CYP1B1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40328000-40365600	Weak transcription	Brain Germinal Matrix	brain
2	chr2:40349800-40358200	Enhancers	Osteobl	bone
3	chr2:40349800-40359600	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr2:40350200-40358000	Enhancers	Muscle Satellite Cultured Cells	--
5	chr2:40351000-40358200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr2:40351200-40358000	Enhancers	NHDF-Ad	bronchial
7	chr2:40351600-40360400	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:40352800-40358000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr2:40354000-40358600	Enhancers	Colon Smooth Muscle	Colon
10	chr2:40354400-40358800	Enhancers	Rectal Smooth Muscle	rectum
11	chr2:40354600-40357800	Enhancers	Left Ventricle	heart
12	chr2:40354600-40358000	Enhancers	HSMM	muscle
13	chr2:40354600-40366600	Weak transcription	Lung	lung
14	chr2:40355000-40366200	Weak transcription	Fetal Muscle Trunk	muscle
15	chr2:40355400-40383800	Weak transcription	Small Intestine	intestine
16	chr2:40355800-40357800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr2:40355800-40365600	Weak transcription	Fetal Muscle Leg	muscle
18	chr2:40355800-40370000	Weak transcription	Fetal Brain Male	brain
19	chr2:40356000-40367400	Weak transcription	Fetal Brain Female	brain
20	chr2:40356400-40357800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:40356600-40358400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:40356800-40358000	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr2:40356800-40358000	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr2:40356800-40358000	Enhancers	Ovary	ovary
25	chr2:40356800-40358200	Enhancers	Stomach Smooth Muscle	stomach
26	chr2:40356800-40358200	Enhancers	NHLF	lung
27	chr2:40356800-40359000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr2:40356800-40375000	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr2:40357000-40357800	Enhancers	Fetal Stomach	stomach
30	chr2:40357000-40358000	Enhancers	Aorta	Aorta
31	chr2:40357000-40358000	Enhancers	Fetal Lung	lung
32	chr2:40357000-40358000	Enhancers	NH-A	brain
33	chr2:40357000-40358200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr2:40357000-40359000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr2:40357200-40357800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:40357200-40357800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:40357200-40358000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr2:40357200-40358000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:40357200-40358400	Weak transcription	Right Atrium	heart
40	chr2:40357400-40357800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr2:40357400-40357800	Enhancers	Brain Anterior Caudate	brain
42	chr2:40357400-40358600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr2:40357600-40357800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr2:40357600-40357800	Strong transcription	Dnd41	blood
45	chr2:40357600-40358000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr2:40357600-40358200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
47	chr2:40357600-40358800	Flanking Active TSS	Fetal Heart	heart
48	chr2:40357600-40359000	Enhancers	Right Ventricle	heart
49	chr2:40357600-40374000	Weak transcription	HSMMtube	muscle

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