Variant report

Variant	rs13025736
Chromosome Location	chr2:50200793-50200794
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10173664	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10185922	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10192677	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10196324	0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11125281	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs12713081	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12713082	0.92[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1421579	0.96[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1421580	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1421599	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1435090	0.89[CEU][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap]
rs1469004	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1543823	0.89[CEU][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2216521	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4971883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6706472	0.96[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3388948	chr2:50092667-50602681	Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
2	esv3399511	chr2:50092687-50602651	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv934303	chr2:50145598-50412189	Bivalent Enhancer Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	2 gene(s)	inside rSNPs	diseases
4	nsv932839	chr2:50181785-50225697	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13025736	SOCS5	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:50198800-50201800	Active TSS	Brain Angular Gyrus	brain
2	chr2:50199200-50200800	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr2:50199200-50201400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:50199200-50201400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:50199400-50200800	Enhancers	Fetal Brain Male	brain
6	chr2:50199400-50201000	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr2:50199400-50201000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr2:50199600-50200800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr2:50199600-50200800	Enhancers	Brain Substantia Nigra	brain
10	chr2:50199600-50201200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:50199600-50201600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
12	chr2:50199600-50201800	Active TSS	Brain Inferior Temporal Lobe	brain
13	chr2:50199800-50201000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
14	chr2:50199800-50201000	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr2:50199800-50201800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr2:50199800-50201800	Active TSS	Brain Anterior Caudate	brain
17	chr2:50199800-50201800	Active TSS	Brain Cingulate Gyrus	brain
18	chr2:50200000-50201200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
19	chr2:50200000-50201200	Enhancers	Fetal Heart	heart
20	chr2:50200000-50201800	Active TSS	Fetal Brain Female	brain
21	chr2:50200200-50201000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:50200200-50201200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr2:50200200-50201200	Weak transcription	Pancreas	Pancrea
24	chr2:50200400-50201000	Enhancers	iPS-20b Cell Line	embryonic stem cell
25	chr2:50200400-50201000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr2:50200400-50201200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr2:50200600-50200800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr2:50200600-50200800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:50200600-50200800	Flanking Active TSS	Brain Hippocampus Middle	brain
30	chr2:50200600-50201000	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr2:50200600-50201200	Enhancers	H9 Cell Line	embryonic stem cell
32	chr2:50200600-50201200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:50200600-50201200	Active TSS	Right Ventricle	heart
34	chr2:50200600-50201800	Active TSS	Brain Germinal Matrix	brain
35	chr2:50200600-50201800	Active TSS	Fetal Kidney	kidney

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