Variant report

Variant	rs9526792
Chromosome Location	chr13:52295318-52295319
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	chr13:52023064..52027990-chr13:52292653..52297533,6	MCF-7	breast:
2	chr13:52025496..52027333-chr13:52294582..52296334,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236778	Chromatin interaction
ENSG00000102786	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs12856726	0.82[MEX][hapmap]
rs1885855	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs1923874	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4456399	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4533167	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4943008	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.92[MKK][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4943014	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6561644	1.00[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];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7327107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7984225	0.88[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];0.95[TSI][hapmap];0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7988297	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7990679	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]
rs9285179	0.94[ASW][hapmap];0.84[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9535716	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9535720	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9568642	0.87[MEX][hapmap]
rs992583	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][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	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
2	nsv530718	chr13:52291802-52832752	Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv933424	chr13:52293482-52507732	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9526792	TNNI2	trans	parietal	SCAN
rs9526792	NCRNA00282	cis	parietal	SCAN

Chromatin state (count:96 , 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	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr13:52263400-52295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr13:52264000-52300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr13:52273600-52295600	Weak transcription	Pancreas	Pancrea
10	chr13:52273600-52295800	Weak transcription	Spleen	Spleen
11	chr13:52274000-52295600	Weak transcription	Ovary	ovary
12	chr13:52274000-52300400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:52276400-52295400	Weak transcription	Adipose Nuclei	Adipose
14	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr13:52277000-52300000	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr13:52278400-52299600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr13:52278800-52301800	Weak transcription	Thymus	Thymus
18	chr13:52278800-52302200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
19	chr13:52279400-52300200	Weak transcription	Liver	Liver
20	chr13:52279400-52301800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:52279400-52301800	Weak transcription	Gastric	stomach
22	chr13:52279400-52303000	Weak transcription	Lung	lung
23	chr13:52279600-52299400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr13:52279600-52300000	Weak transcription	Primary T helper cells fromperipheralblood	blood
25	chr13:52279600-52301800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr13:52279600-52301800	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr13:52279600-52304000	Weak transcription	Esophagus	oesophagus
28	chr13:52280200-52301600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:52282000-52302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr13:52283600-52297200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:52284800-52301000	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr13:52287800-52295600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr13:52288400-52322200	Weak transcription	K562	blood
34	chr13:52288600-52303000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr13:52289000-52300200	Weak transcription	Hela-S3	cervix
36	chr13:52289000-52301800	Weak transcription	A549	lung
37	chr13:52289200-52300000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr13:52289400-52305800	Weak transcription	Fetal Kidney	kidney
39	chr13:52290000-52300400	Weak transcription	NH-A	brain
40	chr13:52290000-52307600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr13:52290200-52301600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr13:52291400-52295400	Strong transcription	HepG2	liver
43	chr13:52291400-52297200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:52291400-52303000	Weak transcription	Fetal Stomach	stomach
45	chr13:52291600-52296400	Enhancers	Brain Substantia Nigra	brain
46	chr13:52292000-52295400	Weak transcription	Aorta	Aorta
47	chr13:52292200-52298200	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr13:52292200-52301800	Weak transcription	Dnd41	blood
49	chr13:52292200-52302600	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr13:52292200-52304400	Weak transcription	Fetal Muscle Trunk	muscle

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