Variant report

Variant	rs13409965
Chromosome Location	chr2:40387388-40387389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11674059	0.83[GIH][hapmap];0.80[TSI][hapmap]
rs13385233	0.83[GIH][hapmap]
rs13399582	0.93[ASN][1000 genomes]
rs13402735	0.81[ASW][hapmap];0.86[TSI][hapmap]
rs1861427	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2058693	0.80[TSI][hapmap]
rs375311	0.80[CHB][hapmap]
rs409620	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs4140823	0.80[GIH][hapmap];0.86[TSI][hapmap]
rs5543	0.81[GIH][hapmap]
rs57603408	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66600435	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13409965	CYP1B1	cis	parietal	SCAN

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40357800-40406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:40358000-40392200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr2:40358200-40392200	Weak transcription	NHLF	lung
4	chr2:40358800-40389200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:40359000-40387400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:40365200-40396200	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr2:40366600-40403000	Weak transcription	Brain Germinal Matrix	brain
8	chr2:40366800-40391800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr2:40369600-40391600	Weak transcription	Rectal Smooth Muscle	rectum
10	chr2:40371800-40391800	Weak transcription	NHDF-Ad	bronchial
11	chr2:40375600-40401800	Weak transcription	HSMMtube	muscle
12	chr2:40376800-40394200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr2:40378000-40391200	Weak transcription	Brain Anterior Caudate	brain
14	chr2:40378000-40391200	Weak transcription	Fetal Thymus	thymus
15	chr2:40378000-40399000	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr2:40378200-40392000	Weak transcription	Gastric	stomach
17	chr2:40379200-40393400	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr2:40381200-40391800	Weak transcription	Adipose Nuclei	Adipose
19	chr2:40381400-40390200	Weak transcription	Fetal Intestine Small	intestine
20	chr2:40381600-40398800	Weak transcription	Brain Angular Gyrus	brain
21	chr2:40381800-40395200	Weak transcription	Spleen	Spleen
22	chr2:40382400-40392800	Strong transcription	Dnd41	blood
23	chr2:40382600-40391800	Strong transcription	Left Ventricle	heart
24	chr2:40382800-40391400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr2:40383000-40387800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr2:40383000-40392400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:40383200-40387800	Weak transcription	Brain Substantia Nigra	brain
28	chr2:40383400-40387400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr2:40383400-40392200	Weak transcription	Aorta	Aorta
30	chr2:40383400-40392600	Strong transcription	HSMM	muscle
31	chr2:40384200-40392200	Weak transcription	Fetal Kidney	kidney
32	chr2:40384600-40391800	Weak transcription	Right Ventricle	heart
33	chr2:40385000-40387400	Weak transcription	Fetal Stomach	stomach
34	chr2:40385000-40389800	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:40385000-40391200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr2:40385800-40387800	Strong transcription	Osteobl	bone
37	chr2:40386000-40388600	Strong transcription	Fetal Heart	heart
38	chr2:40386000-40391600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr2:40386000-40395200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:40386000-40395200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:40386200-40390600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:40386400-40387400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:40386400-40392200	Weak transcription	Fetal Brain Male	brain
44	chr2:40386400-40392200	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:40386400-40395200	Weak transcription	Fetal Intestine Large	intestine
46	chr2:40387000-40387800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:40387000-40387800	Strong transcription	Placenta	Placenta
48	chr2:40387000-40388200	Weak transcription	Fetal Brain Female	brain
49	chr2:40387000-40389800	Weak transcription	Liver	Liver
50	chr2:40387000-40391400	Strong transcription	Colon Smooth Muscle	Colon

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