Variant report

Variant	rs3099359
Chromosome Location	chr13:96485417-96485418
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96484418..96486030-chr13:96489191..96491096,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12583795	0.81[CHB][hapmap]
rs12583796	0.81[CHB][hapmap]
rs1596710	0.96[CEU][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1807900	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs1980942	0.82[ASW][hapmap];0.81[YRI][hapmap]
rs2389530	0.84[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3099357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3099358	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs3099360	0.82[ASW][hapmap]
rs3125433	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3125438	0.84[EUR][1000 genomes]
rs34482628	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34859372	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3901894	0.81[CHB][hapmap]
rs473930	0.86[YRI][hapmap]
rs4773927	0.90[ASW][hapmap];0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4773930	0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs509572	0.89[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs521235	0.81[YRI][hapmap]
rs541811	0.90[ASW][hapmap];0.86[YRI][hapmap]
rs544080	0.86[YRI][hapmap]
rs595696	0.89[CHB][hapmap]
rs6492820	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6492821	0.81[CHB][hapmap]
rs6492826	0.81[YRI][hapmap]
rs7333045	0.81[YRI][hapmap]
rs7334552	0.81[CHB][hapmap]
rs7338266	0.81[CHB][hapmap]
rs7983756	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs7994626	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7998903	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs816139	0.82[ASW][hapmap];0.85[YRI][hapmap]
rs9302083	0.85[JPT][hapmap]
rs9302084	0.83[CEU][hapmap]
rs9516620	0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9525085	0.90[ASW][hapmap];0.81[YRI][hapmap]
rs9525091	0.86[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs9525095	0.82[ASW][hapmap];0.81[YRI][hapmap]
rs9561930	0.87[JPT][hapmap]
rs9561931	0.81[CHB][hapmap]
rs9561939	0.80[CHB][hapmap]
rs9561949	0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	esv3509289	chr13:96461000-96505090	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	esv3509290	chr13:96461000-96505090	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv832691	chr13:96478098-96659823	Strong transcription Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3099359	UGGT2	cis	Muscle Skeletal	GTEx
rs3099359	DZIP1	cis	parietal	SCAN
rs3099359	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL
rs3099359	MIR17HG	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96444400-96485600	Weak transcription	NHDF-Ad	bronchial
2	chr13:96445800-96490000	Weak transcription	HepG2	liver
3	chr13:96452000-96490600	Weak transcription	Fetal Kidney	kidney
4	chr13:96462600-96485600	Weak transcription	Hela-S3	cervix
5	chr13:96466400-96486000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:96466600-96485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr13:96466800-96485800	Weak transcription	Brain Anterior Caudate	brain
8	chr13:96467400-96490800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:96468200-96489800	Weak transcription	GM12878-XiMat	blood
10	chr13:96468800-96486000	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr13:96475800-96485600	Weak transcription	HMEC	breast
12	chr13:96476000-96502600	Weak transcription	Fetal Heart	heart
13	chr13:96476400-96489800	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr13:96477400-96486000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr13:96478000-96485600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr13:96478000-96485600	Weak transcription	Brain Cingulate Gyrus	brain
17	chr13:96478000-96486000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr13:96478000-96486000	Weak transcription	Adipose Nuclei	Adipose
19	chr13:96478000-96498200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr13:96478000-96502600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr13:96478000-96502600	Weak transcription	Left Ventricle	heart
22	chr13:96478000-96568400	Weak transcription	Placenta	Placenta
23	chr13:96478200-96485600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:96478200-96485600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr13:96478200-96485600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr13:96478200-96485600	Weak transcription	NHLF	lung
27	chr13:96478200-96485600	Weak transcription	Osteobl	bone
28	chr13:96478200-96485800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr13:96478200-96485800	Weak transcription	NH-A	brain
30	chr13:96478200-96486000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
31	chr13:96478200-96486000	Weak transcription	Brain Inferior Temporal Lobe	brain
32	chr13:96478200-96486000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr13:96478200-96486400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr13:96478200-96489200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr13:96478200-96489800	Weak transcription	Fetal Intestine Large	intestine
36	chr13:96478200-96489800	Weak transcription	Fetal Muscle Leg	muscle
37	chr13:96478200-96490000	Weak transcription	Brain Hippocampus Middle	brain
38	chr13:96478200-96490400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr13:96478200-96490400	Weak transcription	Liver	Liver
40	chr13:96478200-96490600	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:96478200-96493600	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr13:96478200-96495000	Weak transcription	Lung	lung
43	chr13:96478200-96502200	Weak transcription	Stomach Smooth Muscle	stomach
44	chr13:96478200-96502600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:96478200-96502600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr13:96478200-96502600	Weak transcription	Aorta	Aorta
47	chr13:96478200-96502600	Weak transcription	Fetal Stomach	stomach
48	chr13:96478200-96502600	Weak transcription	Gastric	stomach
49	chr13:96478200-96502600	Weak transcription	Ovary	ovary
50	chr13:96478600-96485600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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