Variant report

Variant	rs1123965
Chromosome Location	chr5:94789177-94789178
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	chr5:94787545..94789529-chr5:94790641..94792240,2	K562	blood:
2	chr5:94788029..94790284-chr5:94790641..94792181,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1162859	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13162779	0.91[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2059786	0.92[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560256	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2560275	0.81[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2560276	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2560277	0.92[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2731816	0.85[YRI][hapmap]
rs2731818	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2731828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2731838	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4573018	0.81[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.83[EUR][1000 genomes]
rs6556871	0.95[CHB][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.83[MKK][hapmap];0.81[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs6556872	0.81[AFR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882388	chr5:94764006-94925849	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv598954	chr5:94783175-94859599	ZNF genes & repeats Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1123965	TTC37	cis	Whole Blood	GTEx
rs1123965	TTC37	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:94777000-94798600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr5:94780400-94810800	Weak transcription	Pancreas	Pancrea
3	chr5:94782000-94810200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr5:94782600-94800000	Weak transcription	HMEC	breast
5	chr5:94783200-94796000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr5:94783400-94795000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr5:94783400-94795800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr5:94783400-94798600	Weak transcription	Gastric	stomach
9	chr5:94783400-94798600	Weak transcription	Left Ventricle	heart
10	chr5:94783600-94797200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr5:94783600-94798400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr5:94785000-94798600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:94785000-94798600	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:94785200-94796000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr5:94785200-94796000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:94785200-94796200	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr5:94785600-94795800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr5:94788400-94811200	Weak transcription	Small Intestine	intestine
19	chr5:94788600-94798600	Weak transcription	Lung	lung
20	chr5:94788800-94822000	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr5:94789000-94798600	Weak transcription	Brain Inferior Temporal Lobe	brain

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