Variant report

Variant	rs3874239
Chromosome Location	chr15:45331689-45331690
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11070436	1.00[CEU][hapmap]
rs11070439	1.00[CEU][hapmap]
rs11634731	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11635836	1.00[CEU][hapmap]
rs11636558	1.00[CEU][hapmap]
rs11637679	1.00[CEU][hapmap]
rs12441189	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs12902975	1.00[CEU][hapmap]
rs12903829	0.94[ASN][1000 genomes]
rs12913288	1.00[CEU][hapmap]
rs13380326	1.00[CEU][hapmap]
rs199138	0.82[CHB][hapmap]
rs2036831	1.00[CEU][hapmap]
rs2437866	1.00[CHB][hapmap];0.86[EUR][1000 genomes]
rs2467841	0.90[EUR][1000 genomes]
rs2467843	0.86[EUR][1000 genomes]
rs2470658	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2470686	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[EUR][1000 genomes]
rs2554451	0.82[CHB][hapmap]
rs269863	0.82[CHB][hapmap]
rs269868	0.82[CHB][hapmap]
rs2854446	0.82[EUR][1000 genomes]
rs35628479	0.88[EUR][1000 genomes]
rs3759890	1.00[CEU][hapmap]
rs452762	1.00[CEU][hapmap]
rs4775707	0.88[EUR][1000 genomes]
rs58232764	0.82[EUR][1000 genomes]
rs6493131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7165595	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7167120	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs925350	1.00[CEU][hapmap]
rs963002	1.00[CEU][hapmap]

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	esv2758380	chr15:44968868-45422842	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	esv2760029	chr15:44968868-45422842	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
3	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv2757599	chr15:45100852-45383620	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv977710	chr15:45316191-45360995	Strong transcription Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
7	esv3438009	chr15:45329164-45353245	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3874239	SORD	cis	Skin Sun Exposed Lower leg	GTEx
rs3874239	CTD-2008A1.2	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45316200-45340600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45316400-45333000	Weak transcription	Lung	lung
3	chr15:45316400-45341200	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:45316400-45342200	Weak transcription	HSMMtube	muscle
5	chr15:45316400-45342600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr15:45316600-45339200	Weak transcription	Fetal Lung	lung
7	chr15:45316600-45340000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr15:45316600-45340600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr15:45316600-45340600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr15:45316600-45344200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr15:45316600-45351000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:45316600-45356600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:45316600-45366600	Weak transcription	Duodenum Smooth Muscle	Duodenum
14	chr15:45316800-45337600	Weak transcription	GM12878-XiMat	blood
15	chr15:45316800-45340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr15:45316800-45346400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr15:45319200-45363200	Weak transcription	Fetal Thymus	thymus
18	chr15:45319800-45339800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr15:45319800-45340600	Weak transcription	Right Ventricle	heart
20	chr15:45319800-45363600	Weak transcription	Brain Angular Gyrus	brain
21	chr15:45322000-45339600	Weak transcription	Ovary	ovary
22	chr15:45322000-45340600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr15:45322000-45340600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:45322000-45340600	Weak transcription	Primary T cells from cord blood	blood
25	chr15:45322000-45341000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr15:45322200-45339600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:45322200-45339800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr15:45322400-45335200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:45322600-45340400	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:45322600-45340600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:45323400-45340000	Weak transcription	NHEK	skin
32	chr15:45323600-45332600	Weak transcription	Dnd41	blood
33	chr15:45323600-45332800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr15:45323600-45341000	Weak transcription	Left Ventricle	heart
35	chr15:45323800-45333600	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr15:45323800-45336000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
37	chr15:45323800-45336800	Weak transcription	Fetal Stomach	stomach
38	chr15:45323800-45337000	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:45323800-45337000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:45323800-45338600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr15:45323800-45338800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:45323800-45339800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:45323800-45340000	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr15:45323800-45340000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:45323800-45340600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:45323800-45342600	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr15:45324000-45336400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr15:45325800-45332000	Enhancers	Liver	Liver
49	chr15:45327000-45333000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:45327600-45340600	Weak transcription	Brain Germinal Matrix	brain

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