Variant report

Variant	rs9548902
Chromosome Location	chr13:40303713-40303714
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40297835..40300183-chr13:40302269..40304121,2	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs12584772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012147	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012153	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3012154	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4303351	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs4329796	0.81[AMR][1000 genomes]
rs4346098	0.83[AMR][1000 genomes]
rs4603426	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56322803	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563751	0.80[EUR][1000 genomes]
rs6650473	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7329513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988187	0.81[AMR][1000 genomes]
rs7989518	0.81[AMR][1000 genomes]
rs7994943	0.83[JPT][hapmap]
rs9532423	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532435	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9548886	0.81[AMR][1000 genomes]
rs9548889	0.81[AMR][1000 genomes]
rs9548899	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548904	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548921	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548923	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548925	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9576885	0.81[AMR][1000 genomes]
rs9576886	0.81[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1054600	chr13:39801283-40545027	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1054797	chr13:40198744-40618428	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
3	nsv541755	chr13:40198744-40618428	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
4	nsv832586	chr13:40222880-40379063	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1040458	chr13:40249387-40638129	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv471130	chr13:40261945-40350912	Strong transcription Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9548902	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
3	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
4	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
5	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr13:40282400-40310800	Weak transcription	Right Ventricle	heart
9	chr13:40283600-40310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr13:40283600-40311000	Weak transcription	Gastric	stomach
11	chr13:40284200-40310400	Weak transcription	Fetal Stomach	stomach
12	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
13	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
14	chr13:40287400-40311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr13:40287400-40311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:40287400-40313000	Weak transcription	NHEK	skin
17	chr13:40287600-40310800	Weak transcription	HSMMtube	muscle
18	chr13:40290200-40311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr13:40291400-40310800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr13:40292000-40310400	Weak transcription	Fetal Brain Female	brain
22	chr13:40292000-40313400	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr13:40292200-40311400	Weak transcription	Fetal Thymus	thymus
24	chr13:40292400-40314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr13:40292600-40310600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr13:40292600-40310800	Weak transcription	Fetal Muscle Leg	muscle
27	chr13:40292800-40307200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:40293400-40312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr13:40294200-40305000	Weak transcription	Left Ventricle	heart
32	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
33	chr13:40294400-40304000	Strong transcription	Primary T cells fromperipheralblood	blood
34	chr13:40294600-40327800	Weak transcription	NH-A	brain
35	chr13:40295600-40311200	Weak transcription	Spleen	Spleen
36	chr13:40295800-40308800	Weak transcription	HepG2	liver
37	chr13:40295800-40311000	Weak transcription	Pancreas	Pancrea
38	chr13:40296200-40311200	Weak transcription	Brain Angular Gyrus	brain
39	chr13:40296600-40304000	Strong transcription	Monocytes-CD14+_RO01746	blood
40	chr13:40296600-40312800	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:40297000-40304000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr13:40297400-40304000	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr13:40297400-40306800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr13:40297600-40310800	Weak transcription	Primary T cells from cord blood	blood
45	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:40297800-40309000	Weak transcription	Brain Substantia Nigra	brain
47	chr13:40297800-40310800	Weak transcription	Fetal Kidney	kidney
48	chr13:40297800-40310800	Weak transcription	Ovary	ovary
49	chr13:40297800-40313000	Weak transcription	Brain Cingulate Gyrus	brain
50	chr13:40297800-40329800	Weak transcription	Brain Inferior Temporal Lobe	brain

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