Variant report

Variant	rs9463997
Chromosome Location	chr6:53769820-53769821
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	chr6:53768489..53771106-chr6:53771711..53773800,2	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10456168	0.82[EUR][1000 genomes]
rs10755768	0.88[EUR][1000 genomes]
rs12661938	0.83[ASN][1000 genomes]
rs12663216	0.89[JPT][hapmap]
rs2006013	0.80[EUR][1000 genomes]
rs2050159	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2820218	0.93[YRI][hapmap]
rs3003492	0.88[JPT][hapmap]
rs3003498	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs34299171	0.80[EUR][1000 genomes]
rs35081045	0.84[EUR][1000 genomes]
rs4273680	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs4486000	0.84[CHD][hapmap];0.89[JPT][hapmap]
rs4582388	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4715428	0.84[EUR][1000 genomes]
rs4715429	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62397090	0.88[ASN][1000 genomes]
rs6458973	0.89[EUR][1000 genomes]
rs6902746	0.80[EUR][1000 genomes]
rs6905323	0.83[ASN][1000 genomes]
rs6905563	0.82[JPT][hapmap]
rs6906326	1.00[CEU][hapmap];0.89[JPT][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6907354	0.89[EUR][1000 genomes]
rs6916929	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6925391	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6935942	0.82[EUR][1000 genomes]
rs7744962	0.80[EUR][1000 genomes]
rs7750173	0.90[ASN][1000 genomes]
rs7769351	0.80[EUR][1000 genomes]
rs7773779	0.80[EUR][1000 genomes]
rs9357777	0.87[EUR][1000 genomes]
rs9370245	0.88[EUR][1000 genomes]
rs9395890	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs9395891	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs9463988	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9463996	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9474671	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9474672	0.94[LWK][hapmap];0.96[YRI][hapmap]
rs9474680	0.94[AMR][1000 genomes];0.99[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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1021506	chr6:53600338-53770482	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9463997	PAQR8	cis	parietal	SCAN
rs9463997	LRRC1	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53739000-53771800	Weak transcription	Pancreas	Pancrea
2	chr6:53752400-53771000	Weak transcription	Gastric	stomach
3	chr6:53752400-53771800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr6:53752800-53782000	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr6:53754800-53775600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr6:53754800-53779800	Weak transcription	NHLF	lung
7	chr6:53755000-53779800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr6:53756000-53781800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr6:53758000-53775600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:53759200-53770800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr6:53759200-53787600	Weak transcription	Spleen	Spleen
12	chr6:53759200-53794400	Weak transcription	Right Ventricle	heart
13	chr6:53759400-53770000	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr6:53759400-53771800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr6:53759400-53786400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr6:53759600-53789800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr6:53760400-53789400	Weak transcription	Stomach Mucosa	stomach
18	chr6:53760400-53791200	Weak transcription	Hela-S3	cervix
19	chr6:53760600-53773000	Strong transcription	Dnd41	blood
20	chr6:53760600-53778800	Weak transcription	Fetal Muscle Leg	muscle
21	chr6:53760600-53793600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:53760800-53771800	Weak transcription	Brain Angular Gyrus	brain
23	chr6:53761000-53770800	Weak transcription	Brain Substantia Nigra	brain
24	chr6:53761000-53771200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr6:53761000-53771600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr6:53761000-53771800	Weak transcription	Brain Anterior Caudate	brain
27	chr6:53761000-53782000	Weak transcription	Fetal Kidney	kidney
28	chr6:53761000-53782800	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr6:53761000-53785400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr6:53761400-53771800	Weak transcription	HUES64 Cell Line	embryonic stem cell
31	chr6:53761400-53776400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr6:53761400-53787400	Weak transcription	HMEC	breast
33	chr6:53761400-53791200	Weak transcription	Colon Smooth Muscle	Colon
34	chr6:53761600-53771000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr6:53761600-53790800	Weak transcription	Fetal Heart	heart
36	chr6:53761800-53772400	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr6:53761800-53777000	Strong transcription	Fetal Thymus	thymus
38	chr6:53761800-53786800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr6:53762000-53774000	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr6:53762000-53775600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr6:53762000-53791200	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:53762000-53791600	Weak transcription	Fetal Lung	lung
43	chr6:53762200-53786800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr6:53762800-53775600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr6:53763000-53772200	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr6:53764000-53772000	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr6:53764000-53772000	Strong transcription	HSMMtube	muscle
48	chr6:53764200-53772000	Strong transcription	Fetal Intestine Small	intestine
49	chr6:53764400-53784600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr6:53765800-53771400	Strong transcription	HepG2	liver

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