Variant report

Variant	rs12583796
Chromosome Location	chr13:96433582-96433583
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	chr13:96431368..96434044-chr13:96435858..96438220,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12430152	0.93[YRI][hapmap]
rs12583795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12855055	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17878753	0.81[AFR][1000 genomes]
rs2389530	0.81[CHB][hapmap]
rs3099357	0.81[CHB][hapmap]
rs3099359	0.81[CHB][hapmap]
rs3101570	0.84[LWK][hapmap];1.00[YRI][hapmap]
rs35740456	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3848077	0.82[AFR][1000 genomes]
rs3886352	0.86[LWK][hapmap];0.96[YRI][hapmap]
rs3901894	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4409947	1.00[YRI][hapmap]
rs59576762	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6492820	0.90[CHB][hapmap]
rs6492821	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7316996	0.96[YRI][hapmap]
rs7318892	0.93[YRI][hapmap]
rs7323408	0.93[YRI][hapmap]
rs7331211	0.89[YRI][hapmap]
rs7331549	0.93[YRI][hapmap]
rs7334552	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338266	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7983756	0.90[CHB][hapmap]
rs7991405	0.93[YRI][hapmap]
rs7995306	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9302084	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9561925	0.88[CEU][hapmap]
rs9561931	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9561935	0.89[CEU][hapmap]
rs9561936	0.89[CEU][hapmap]
rs9561939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9561953	0.92[CEU][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9584324	1.00[YRI][hapmap]
rs9584326	0.90[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12583796	UGCGL2	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96367600-96436000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:96394000-96435800	Weak transcription	A549	lung
3	chr13:96394400-96438400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr13:96394600-96435800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:96398400-96436200	Weak transcription	Colon Smooth Muscle	Colon
6	chr13:96398400-96439400	Weak transcription	Brain Hippocampus Middle	brain
7	chr13:96404000-96439400	Weak transcription	Thymus	Thymus
8	chr13:96405400-96436800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr13:96405400-96439400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr13:96405400-96452600	Weak transcription	Psoas Muscle	Psoas
11	chr13:96405600-96455800	Weak transcription	Fetal Heart	heart
12	chr13:96406600-96435800	Weak transcription	Gastric	stomach
13	chr13:96406600-96436000	Weak transcription	NHLF	lung
14	chr13:96406800-96435800	Weak transcription	Pancreas	Pancrea
15	chr13:96407200-96439400	Weak transcription	Brain Anterior Caudate	brain
16	chr13:96408400-96443600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr13:96408600-96443200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr13:96408600-96445400	Weak transcription	K562	blood
19	chr13:96409800-96434200	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr13:96410400-96436200	Weak transcription	Aorta	Aorta
21	chr13:96411400-96439400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:96412000-96443400	Weak transcription	Colonic Mucosa	Colon
23	chr13:96413200-96439800	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr13:96414000-96435800	Weak transcription	Right Ventricle	heart
25	chr13:96414000-96436600	Weak transcription	Rectal Smooth Muscle	rectum
26	chr13:96414000-96443400	Weak transcription	Brain Angular Gyrus	brain
27	chr13:96414400-96443400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr13:96415600-96439400	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr13:96416200-96433600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr13:96416200-96436400	Weak transcription	HSMMtube	muscle
31	chr13:96416200-96439200	Weak transcription	Brain Substantia Nigra	brain
32	chr13:96416200-96439200	Weak transcription	Fetal Muscle Trunk	muscle
33	chr13:96416200-96443400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr13:96416200-96445400	Weak transcription	Fetal Kidney	kidney
35	chr13:96416400-96440000	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr13:96416400-96440200	Weak transcription	HepG2	liver
37	chr13:96416800-96436200	Weak transcription	Placenta	Placenta
38	chr13:96417600-96435800	Weak transcription	HUVEC	blood vessel
39	chr13:96417600-96435800	Weak transcription	NHEK	skin
40	chr13:96417600-96436000	Weak transcription	NH-A	brain
41	chr13:96417600-96438400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
42	chr13:96417600-96439400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr13:96417600-96439400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:96417800-96436000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr13:96418800-96436200	Weak transcription	HMEC	breast
46	chr13:96419800-96435800	Weak transcription	Osteobl	bone
47	chr13:96420600-96434200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr13:96422200-96440600	Weak transcription	Fetal Lung	lung
49	chr13:96422400-96439400	Weak transcription	Small Intestine	intestine
50	chr13:96423800-96436000	Weak transcription	HSMM	muscle

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