Variant report

Variant	rs2241826
Chromosome Location	chr5:79354184-79354185
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79342559..79344595-chr5:79353378..79355370,2	MCF-7	breast:

Extended variants
information (count: 21 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10071934	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10474606	0.80[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10514171	0.87[CHB][hapmap]
rs10514174	0.94[CHB][hapmap]
rs11738491	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11739940	0.91[ASN][1000 genomes]
rs12332694	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13181102	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16877406	0.87[CHB][hapmap]
rs16877442	1.00[CHB][hapmap]
rs16877468	1.00[CHB][hapmap]
rs17878919	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3813667	0.91[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4703797	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7723567	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.89[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9293797	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9293799	0.95[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9293800	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
2	nsv882223	chr5:79330559-79357117	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv882230	chr5:79351544-79354647	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2241826	THBS4	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79338200-79363600	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr5:79338200-79367600	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr5:79338400-79355200	Weak transcription	Brain Anterior Caudate	brain
4	chr5:79339200-79354600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr5:79340000-79363400	Weak transcription	Left Ventricle	heart
6	chr5:79344200-79355200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:79345200-79364200	Weak transcription	Right Ventricle	heart
8	chr5:79347800-79355600	Weak transcription	Brain Hippocampus Middle	brain
9	chr5:79348200-79366400	Weak transcription	Brain Substantia Nigra	brain
10	chr5:79350600-79363200	Weak transcription	Psoas Muscle	Psoas
11	chr5:79351600-79379200	Weak transcription	Pancreas	Pancrea
12	chr5:79351800-79361800	Weak transcription	Primary T cells from cord blood	blood
13	chr5:79352000-79355600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:79352000-79361200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr5:79352000-79365200	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr5:79352000-79365600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:79352000-79365800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:79352200-79356600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:79352200-79359600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr5:79352400-79378200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:79352600-79356800	Weak transcription	Fetal Heart	heart
22	chr5:79352800-79363400	Weak transcription	Fetal Muscle Trunk	muscle
23	chr5:79353200-79354200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
24	chr5:79353200-79365600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:79353400-79355000	Enhancers	Osteobl	bone
26	chr5:79353600-79363400	Weak transcription	Brain Cingulate Gyrus	brain
27	chr5:79353600-79365600	Weak transcription	Fetal Intestine Small	intestine
28	chr5:79354000-79354800	Enhancers	NHDF-Ad	bronchial
29	chr5:79354000-79355600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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