Variant report

Variant	rs9561930
Chromosome Location	chr13:96342022-96342023
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FOXA1	chr13:96341972-96342213	A549	lung:	n/a	n/a
2	FOXA1	chr13:96341836-96342219	HepG2	liver:	n/a	n/a
3	FOXA1	chr13:96341876-96342296	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
MTCYBP3	TF binding region
MTND5P2	TF binding region

Extended variants
information (count: 11 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs3099357	0.87[JPT][hapmap]
rs3099359	0.87[JPT][hapmap]
rs4773927	0.87[JPT][hapmap]
rs6492818	0.92[LWK][hapmap];1.00[YRI][hapmap]
rs6492820	0.87[JPT][hapmap]
rs7983756	0.87[JPT][hapmap]
rs7998903	0.86[JPT][hapmap]
rs9302083	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9516620	0.94[JPT][hapmap]
rs9584326	0.81[CHB][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	nsv832690	chr13:96330757-96508077	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9561930	UGCGL2	cis	multi-tissue	Pritchard
rs9561930	MIR17HG	cis	cerebellum	SCAN
rs9561930	DZIP1	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96331400-96350600	Weak transcription	Aorta	Aorta
2	chr13:96331400-96362200	Weak transcription	HSMM	muscle
3	chr13:96332000-96348000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr13:96332400-96360400	Weak transcription	NHDF-Ad	bronchial
5	chr13:96332600-96350200	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr13:96334800-96344400	Weak transcription	Colon Smooth Muscle	Colon
7	chr13:96337400-96346400	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr13:96337400-96347600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr13:96337400-96350400	Weak transcription	Lung	lung
10	chr13:96337600-96346200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr13:96337600-96347200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:96337600-96347800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:96337600-96348400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:96337600-96350400	Weak transcription	Pancreas	Pancrea
15	chr13:96337600-96350400	Weak transcription	Right Ventricle	heart
16	chr13:96337600-96350400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr13:96337600-96350400	Weak transcription	Small Intestine	intestine
18	chr13:96337600-96356000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:96337600-96358800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr13:96337600-96360800	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr13:96337600-96362200	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr13:96337600-96364200	Weak transcription	Ovary	ovary
23	chr13:96340400-96342200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr13:96340600-96342200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr13:96341000-96342200	Enhancers	Primary T helper naive cells from peripheral blood	blood
26	chr13:96341000-96342200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
27	chr13:96341000-96350600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr13:96341200-96350400	Weak transcription	Psoas Muscle	Psoas
29	chr13:96341200-96350400	Weak transcription	Right Atrium	heart
30	chr13:96341400-96345000	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr13:96341600-96342200	Enhancers	HepG2	liver
32	chr13:96341800-96342200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr13:96341800-96342200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr13:96342000-96346600	Weak transcription	GM12878-XiMat	blood
35	chr13:96342000-96350400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr13:96342000-96350400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr13:96342000-96350600	Weak transcription	Liver	Liver

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