Variant report

Variant	rs9590328
Chromosome Location	chr13:96448383-96448384
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	chr13:96447571..96450064-chr13:96451642..96454530,2	K562	blood:

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10508027	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs11616953	1.00[ASN][1000 genomes]
rs11618323	0.89[ASN][1000 genomes]
rs12430152	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[TSI][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12583796	1.00[YRI][hapmap]
rs16951334	0.82[CHD][hapmap]
rs17878753	0.81[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs17879875	0.83[ASN][1000 genomes]
rs1788062	1.00[JPT][hapmap]
rs17885081	0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1854758	1.00[JPT][hapmap]
rs3087341	0.92[ASN][1000 genomes]
rs3099362	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs3099363	1.00[JPT][hapmap]
rs3101570	0.94[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.80[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3125431	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs3848077	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs3886352	0.87[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.86[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3901894	1.00[YRI][hapmap]
rs4383020	0.88[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs4409947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4491364	0.97[ASN][1000 genomes]
rs6492817	0.88[CEU][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs6492821	1.00[YRI][hapmap]
rs6492822	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7316996	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7318892	0.87[ASW][hapmap];0.87[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs7323408	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7331211	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7331549	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7332078	1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs7334320	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7334552	1.00[YRI][hapmap]
rs7335209	0.80[EUR][1000 genomes]
rs7339059	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7991405	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.85[AMR][1000 genomes]
rs7999737	1.00[JPT][hapmap]
rs8000018	0.87[EUR][1000 genomes]
rs816142	0.91[CHD][hapmap];0.86[JPT][hapmap]
rs9302084	1.00[YRI][hapmap]
rs9516621	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9525079	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9561931	0.89[YRI][hapmap]
rs9561939	0.96[YRI][hapmap]
rs9584324	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9590310	0.85[AMR][1000 genomes]
rs9590316	0.84[EUR][1000 genomes]
rs9590318	0.88[CEU][hapmap];0.89[TSI][hapmap];0.84[EUR][1000 genomes]
rs9590321	0.84[TSI][hapmap];0.84[EUR][1000 genomes]
rs9590331	0.88[CEU][hapmap];0.92[EUR][1000 genomes]

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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9590328	UGGT2	cis	cerebellum	SCAN
rs9590328	DZIP1	cis	parietal	SCAN

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:96405400-96452600	Weak transcription	Psoas Muscle	Psoas
2	chr13:96405600-96455800	Weak transcription	Fetal Heart	heart
3	chr13:96430000-96457400	Weak transcription	Brain Germinal Matrix	brain
4	chr13:96433000-96453000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr13:96436000-96449000	Strong transcription	Primary neutrophils fromperipheralblood	blood
6	chr13:96436200-96452200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr13:96437000-96451400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr13:96437400-96448800	Strong transcription	Liver	Liver
9	chr13:96438200-96450200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:96438800-96451200	Weak transcription	Placenta Amnion	Placenta Amnion
11	chr13:96439400-96449000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr13:96439400-96450400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr13:96439800-96454200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr13:96441800-96450400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr13:96441800-96451400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr13:96443800-96450800	Weak transcription	Spleen	Spleen
17	chr13:96443800-96465600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr13:96443800-96466000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr13:96444400-96449000	Weak transcription	Colonic Mucosa	Colon
20	chr13:96444400-96452200	Weak transcription	Fetal Brain Female	brain
21	chr13:96444400-96453000	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:96444400-96461600	Weak transcription	Esophagus	oesophagus
23	chr13:96444400-96461800	Weak transcription	Ovary	ovary
24	chr13:96444400-96477600	Weak transcription	Brain Angular Gyrus	brain
25	chr13:96444400-96477600	Weak transcription	NHLF	lung
26	chr13:96444400-96485600	Weak transcription	NHDF-Ad	bronchial
27	chr13:96444600-96449200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr13:96445000-96450200	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:96445000-96451800	Weak transcription	A549	lung
30	chr13:96445000-96453000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
31	chr13:96445000-96455800	Weak transcription	HMEC	breast
32	chr13:96445000-96458400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr13:96445200-96451400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr13:96445600-96448600	Weak transcription	Colon Smooth Muscle	Colon
35	chr13:96445600-96449400	Weak transcription	Fetal Thymus	thymus
36	chr13:96445600-96451400	Weak transcription	Fetal Kidney	kidney
37	chr13:96445600-96452200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:96445600-96454800	Weak transcription	Lung	lung
39	chr13:96445600-96461600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr13:96445600-96461800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr13:96445600-96461800	Weak transcription	Pancreas	Pancrea
42	chr13:96445600-96477400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr13:96445800-96448400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr13:96445800-96448400	Weak transcription	Right Ventricle	heart
45	chr13:96445800-96449800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr13:96445800-96450200	Weak transcription	Primary B cells from cord blood	blood
47	chr13:96445800-96453800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr13:96445800-96455400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:96445800-96461600	Weak transcription	Aorta	Aorta
50	chr13:96445800-96490000	Weak transcription	HepG2	liver

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