Variant report

Variant	rs4941696
Chromosome Location	chr13:51897793-51897794
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs2274061	1.00[CEU][hapmap];0.86[GIH][hapmap];0.89[TSI][hapmap];0.85[EUR][1000 genomes]
rs2274929	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3825524	1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs4942989	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4942990	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4942991	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7333661	0.84[EUR][1000 genomes]
rs7989850	0.82[CEU][hapmap]
rs7996243	1.00[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.89[EUR][1000 genomes]
rs7998084	0.82[CEU][hapmap]
rs9316539	0.85[EUR][1000 genomes]
rs9316545	0.82[CEU][hapmap]
rs9526752	1.00[CEU][hapmap];0.89[GIH][hapmap];0.84[MEX][hapmap];0.85[TSI][hapmap];0.85[EUR][1000 genomes]
rs9526754	0.95[CEU][hapmap];0.89[GIH][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs9526764	0.81[CEU][hapmap]
rs9535644	0.88[ASN][1000 genomes]
rs9535645	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9535650	0.81[YRI][hapmap]
rs9535653	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs9535670	0.82[CEU][hapmap]
rs9535696	0.81[CEU][hapmap]
rs9535697	0.81[CEU][hapmap]
rs9568600	0.85[CEU][hapmap]
rs9568603	0.82[CEU][hapmap]
rs9568612	0.82[CEU][hapmap]
rs9596506	0.81[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4941696	HNRNPA1L2	cis	cerebellum	SCAN
rs4941696	INTS6	Cis_1M	lymphoblastoid	RTeQTL
rs4941696	CKAP2	cis	parietal	SCAN
rs4941696	C13orf18	cis	cerebellum	SCAN
rs4941696	SUCLA2	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51867600-51910800	Weak transcription	Pancreas	Pancrea
2	chr13:51889400-51901200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:51890000-51899200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr13:51890000-51904800	Weak transcription	Right Atrium	heart
5	chr13:51890200-51899400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr13:51890600-51898400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr13:51893800-51898400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr13:51894000-51898800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr13:51895600-51898400	Weak transcription	Fetal Muscle Leg	muscle
10	chr13:51895600-51898600	Enhancers	Brain Anterior Caudate	brain
11	chr13:51896200-51898400	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr13:51896200-51898600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:51896400-51898400	Weak transcription	Brain Germinal Matrix	brain
14	chr13:51896600-51899400	Enhancers	Brain Hippocampus Middle	brain
15	chr13:51897000-51898800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr13:51897000-51900400	Enhancers	Brain Substantia Nigra	brain
17	chr13:51897200-51897800	Enhancers	Fetal Muscle Trunk	muscle
18	chr13:51897200-51899200	Enhancers	Brain Cingulate Gyrus	brain
19	chr13:51897400-51898400	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr13:51897400-51898600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr13:51897400-51899200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:51897400-51899400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr13:51897600-51898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:51897600-51898400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr13:51897600-51898400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr13:51897600-51898600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr13:51897600-51904800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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