Variant report

Variant	rs9593081
Chromosome Location	chr13:76049219-76049220
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	chr13:76049073..76053204-chr13:76053601..76056475,3	K562	blood:
2	chr13:76048295..76050774-chr13:76052549..76054947,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000136111	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1050235	0.80[CEU][hapmap]
rs10507830	1.00[CHB][hapmap]
rs11148993	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146901	0.83[EUR][1000 genomes]
rs12146907	0.83[EUR][1000 genomes]
rs12146936	0.81[EUR][1000 genomes]
rs12855863	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs12869081	0.80[CEU][hapmap]
rs1325463	0.87[ASN][1000 genomes]
rs1359502	0.87[ASN][1000 genomes]
rs17064454	1.00[CHB][hapmap]
rs17064554	0.87[ASN][1000 genomes]
rs2031505	1.00[CHB][hapmap]
rs2031506	1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[ASN][1000 genomes]
rs2146981	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825440	0.87[ASN][1000 genomes]
rs4885295	1.00[CHB][hapmap]
rs4885298	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885299	0.86[EUR][1000 genomes]
rs7999938	0.87[ASN][1000 genomes]
rs9318351	0.84[EUR][1000 genomes]
rs9318352	0.87[ASN][1000 genomes]
rs9543938	0.86[CEU][hapmap];0.86[EUR][1000 genomes]
rs9543941	1.00[EUR][1000 genomes]
rs9543942	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9543943	0.93[CEU][hapmap];1.00[EUR][1000 genomes]
rs9543948	0.84[EUR][1000 genomes]
rs9543949	0.84[EUR][1000 genomes]
rs9543952	0.80[CEU][hapmap]
rs9593085	0.81[EUR][1000 genomes]
rs9593086	0.84[EUR][1000 genomes]
rs9600482	0.84[EUR][1000 genomes]
rs9634728	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9634729	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs975435	0.87[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	esv2761803	chr13:75943309-76161774	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv455987	chr13:75972846-76090084	Enhancers Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv562346	chr13:75972846-76090084	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9593081	TBC1D4	cis	cerebellum	SCAN
rs9593081	UCHL3	cis	parietal	SCAN
rs9593081	LMO7	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76020400-76054400	Weak transcription	A549	lung
2	chr13:76028400-76054800	Weak transcription	Esophagus	oesophagus
3	chr13:76031800-76053400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr13:76039400-76052000	Weak transcription	Right Ventricle	heart
5	chr13:76039600-76053600	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr13:76039800-76054200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:76040200-76054800	Weak transcription	Pancreas	Pancrea
8	chr13:76042400-76052000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr13:76043000-76051800	Weak transcription	Liver	Liver
10	chr13:76043000-76053000	Weak transcription	NHDF-Ad	bronchial
11	chr13:76043600-76053600	Weak transcription	Hela-S3	cervix
12	chr13:76043800-76053600	Weak transcription	NHEK	skin
13	chr13:76045800-76052000	Weak transcription	Right Atrium	heart
14	chr13:76045800-76054600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr13:76046000-76052000	Weak transcription	Left Ventricle	heart
16	chr13:76046000-76053600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr13:76047400-76051000	Weak transcription	Ovary	ovary
18	chr13:76047400-76052000	Weak transcription	Psoas Muscle	Psoas
19	chr13:76047400-76052200	Weak transcription	Fetal Muscle Leg	muscle
20	chr13:76048200-76051800	Weak transcription	Adipose Nuclei	Adipose
21	chr13:76048200-76052000	Weak transcription	Fetal Lung	lung
22	chr13:76048400-76049800	Weak transcription	Fetal Heart	heart
23	chr13:76048400-76054200	Weak transcription	Colon Smooth Muscle	Colon
24	chr13:76048800-76049800	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr13:76049000-76050800	Enhancers	HepG2	liver
26	chr13:76049200-76049400	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr13:76049200-76049600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr13:76049200-76049600	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr13:76049200-76049600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr13:76049200-76049600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr13:76049200-76049800	Enhancers	GM12878-XiMat	blood

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