Variant report

Variant	rs7990679
Chromosome Location	chr13:52290309-52290310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12856726	0.82[MEX][hapmap]
rs1885855	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs1923874	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4456399	0.80[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.97[TSI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4533167	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4943008	0.88[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4943014	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6561644	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320201	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7327107	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984225	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9285179	0.88[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9526792	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535716	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9535720	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568642	0.87[MEX][hapmap]
rs992583	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7990679	NCRNA00282	cis	parietal	SCAN
rs7990679	TNNI2	trans	parietal	SCAN

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52247600-52300200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:52247600-52300200	Weak transcription	Fetal Lung	lung
3	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:52254600-52293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:52263400-52295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr13:52264000-52300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:52270400-52293200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr13:52273400-52291800	Weak transcription	Brain Anterior Caudate	brain
12	chr13:52273600-52291400	Weak transcription	Brain Hippocampus Middle	brain
13	chr13:52273600-52293000	Weak transcription	Right Atrium	heart
14	chr13:52273600-52293200	Weak transcription	Left Ventricle	heart
15	chr13:52273600-52295200	Weak transcription	Right Ventricle	heart
16	chr13:52273600-52295600	Weak transcription	Pancreas	Pancrea
17	chr13:52273600-52295800	Weak transcription	Spleen	Spleen
18	chr13:52274000-52295600	Weak transcription	Ovary	ovary
19	chr13:52274000-52300400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr13:52276400-52295400	Weak transcription	Adipose Nuclei	Adipose
21	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:52277000-52300000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr13:52278400-52299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:52278800-52301800	Weak transcription	Thymus	Thymus
25	chr13:52278800-52302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr13:52279400-52291800	Weak transcription	Aorta	Aorta
27	chr13:52279400-52295200	Weak transcription	Stomach Smooth Muscle	stomach
28	chr13:52279400-52300200	Weak transcription	Liver	Liver
29	chr13:52279400-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:52279400-52301800	Weak transcription	Gastric	stomach
31	chr13:52279400-52303000	Weak transcription	Lung	lung
32	chr13:52279600-52293000	Weak transcription	Primary B cells from peripheral blood	blood
33	chr13:52279600-52293200	Weak transcription	Primary T cells from cord blood	blood
34	chr13:52279600-52295000	Weak transcription	HSMMtube	muscle
35	chr13:52279600-52299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr13:52279600-52300000	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr13:52279600-52301800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr13:52279600-52301800	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr13:52279600-52304000	Weak transcription	Esophagus	oesophagus
40	chr13:52280200-52301600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr13:52280400-52291400	Weak transcription	HepG2	liver
42	chr13:52281000-52294800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr13:52281600-52293200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr13:52282000-52302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr13:52283600-52297200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr13:52284800-52301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
47	chr13:52287600-52290400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr13:52287600-52293000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr13:52287800-52295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr13:52288000-52290600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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