Variant report

Variant	rs3099357
Chromosome Location	chr13:96476782-96476783
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:96471414..96473149-chr13:96476270..96478786,2	K562	blood:
2	chr13:96328293..96330323-chr13:96475800..96477548,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000247400	Chromatin interaction
ENSG00000102580	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12583795	0.81[CHB][hapmap]
rs12583796	0.81[CHB][hapmap]
rs1596710	0.96[CEU][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2389530	1.00[ASW][hapmap];0.84[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes]
rs3099358	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs3099359	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]
rs3125433	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3125438	0.86[EUR][1000 genomes]
rs34482628	0.82[EUR][1000 genomes]
rs34859372	0.93[EUR][1000 genomes]
rs3901894	0.81[CHB][hapmap]
rs4773927	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs509572	1.00[ASW][hapmap];0.89[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.85[TSI][hapmap]
rs6492820	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6492821	0.81[CHB][hapmap]
rs7334552	0.81[CHB][hapmap]
rs7338266	0.81[CHB][hapmap]
rs7983756	0.96[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7994626	0.84[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7998903	0.88[CEU][hapmap];0.94[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9302083	0.85[JPT][hapmap]
rs9302084	0.83[CEU][hapmap]
rs9516620	0.88[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs9561930	0.87[JPT][hapmap]
rs9561931	0.81[CHB][hapmap]
rs9561939	0.80[CHB][hapmap]
rs9561949	0.84[AMR][1000 genomes];0.95[EUR][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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3099357	UGGT2	cis	Muscle Skeletal	GTEx
rs3099357	UGCGL2	cis	multi-tissue	Pritchard
rs3099357	MIR17HG	cis	cerebellum	SCAN
rs3099357	DZIP1	cis	parietal	SCAN
rs3099357	UGCGL2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96444400-96477600	Weak transcription	Brain Angular Gyrus	brain
2	chr13:96444400-96477600	Weak transcription	NHLF	lung
3	chr13:96444400-96485600	Weak transcription	NHDF-Ad	bronchial
4	chr13:96445600-96477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:96445800-96490000	Weak transcription	HepG2	liver
6	chr13:96446200-96477400	Weak transcription	Gastric	stomach
7	chr13:96446800-96477400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr13:96446800-96477400	Weak transcription	HSMMtube	muscle
9	chr13:96447200-96477400	Weak transcription	Osteobl	bone
10	chr13:96452000-96490600	Weak transcription	Fetal Kidney	kidney
11	chr13:96458800-96477400	Weak transcription	NH-A	brain
12	chr13:96460400-96477200	Weak transcription	A549	lung
13	chr13:96460400-96477400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr13:96462000-96477400	Weak transcription	HSMM	muscle
15	chr13:96462200-96477200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr13:96462200-96477400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr13:96462600-96485600	Weak transcription	Hela-S3	cervix
18	chr13:96465600-96481200	Weak transcription	Psoas Muscle	Psoas
19	chr13:96466200-96477400	Weak transcription	Fetal Intestine Large	intestine
20	chr13:96466200-96477800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr13:96466200-96480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr13:96466200-96481400	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr13:96466400-96477200	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:96466400-96477400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr13:96466400-96485400	Weak transcription	NHEK	skin
26	chr13:96466400-96486000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr13:96466600-96477200	Weak transcription	Brain Germinal Matrix	brain
28	chr13:96466600-96477200	Weak transcription	Fetal Lung	lung
29	chr13:96466600-96477400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr13:96466600-96477400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr13:96466600-96477400	Weak transcription	Liver	Liver
32	chr13:96466600-96477400	Weak transcription	Left Ventricle	heart
33	chr13:96466600-96477400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr13:96466600-96477400	Weak transcription	Stomach Smooth Muscle	stomach
35	chr13:96466600-96477600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr13:96466600-96477800	Weak transcription	Spleen	Spleen
37	chr13:96466600-96485800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr13:96466800-96477200	Weak transcription	Fetal Brain Female	brain
39	chr13:96466800-96477400	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr13:96466800-96477400	Weak transcription	Brain Cingulate Gyrus	brain
41	chr13:96466800-96477400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr13:96466800-96477400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr13:96466800-96477400	Weak transcription	Fetal Muscle Leg	muscle
44	chr13:96466800-96477400	Weak transcription	Fetal Stomach	stomach
45	chr13:96466800-96477600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr13:96466800-96485800	Weak transcription	Brain Anterior Caudate	brain
47	chr13:96467000-96476800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:96467000-96477200	Weak transcription	Fetal Muscle Trunk	muscle
49	chr13:96467000-96477600	Weak transcription	Right Ventricle	heart
50	chr13:96467000-96485200	Weak transcription	HUVEC	blood vessel

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