Variant report

Variant	rs9548906
Chromosome Location	chr13:40308690-40308691
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11618960	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4133063	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4245396	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs4288869	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4408422	0.88[AFR][1000 genomes]
rs4943694	0.85[AFR][1000 genomes]
rs4943695	0.81[AFR][1000 genomes]
rs4943696	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7319128	0.81[AFR][1000 genomes]
rs7325068	0.88[ASW][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs7327824	0.81[AFR][1000 genomes]
rs7330211	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7334651	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs7998641	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs8000009	0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532429	0.81[AFR][1000 genomes]
rs9548898	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548900	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9548901	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9548905	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548913	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548914	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548916	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548917	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9548918	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548919	0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548920	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs9548922	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548926	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs9548927	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548928	0.81[AFR][1000 genomes]
rs9548930	0.89[YRI][hapmap]
rs9566474	0.81[AFR][1000 genomes]
rs9576891	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs9576892	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs9576894	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9576895	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9576896	0.81[AFR][1000 genomes]
rs9576898	0.81[AFR][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548906	COG6	cis	multi-tissue	Pritchard
rs9548906	COG6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40255800-40340200	Weak transcription	Psoas Muscle	Psoas
2	chr13:40257600-40310800	Weak transcription	Brain Germinal Matrix	brain
3	chr13:40262800-40311000	Weak transcription	Aorta	Aorta
4	chr13:40262800-40311000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr13:40267600-40341200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:40274600-40327000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr13:40282400-40310800	Weak transcription	Right Ventricle	heart
8	chr13:40283600-40310400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr13:40283600-40311000	Weak transcription	Gastric	stomach
10	chr13:40284200-40310400	Weak transcription	Fetal Stomach	stomach
11	chr13:40285200-40317600	Weak transcription	Small Intestine	intestine
12	chr13:40286200-40332200	Weak transcription	Esophagus	oesophagus
13	chr13:40287400-40311000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:40287400-40311400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr13:40287400-40313000	Weak transcription	NHEK	skin
16	chr13:40287600-40310800	Weak transcription	HSMMtube	muscle
17	chr13:40290200-40311000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr13:40290600-40328600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:40291400-40310800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr13:40292000-40310400	Weak transcription	Fetal Brain Female	brain
21	chr13:40292000-40313400	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr13:40292200-40311400	Weak transcription	Fetal Thymus	thymus
23	chr13:40292400-40314800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:40292600-40310600	Weak transcription	Fetal Muscle Trunk	muscle
25	chr13:40292600-40310800	Weak transcription	Fetal Muscle Leg	muscle
26	chr13:40293000-40340800	Weak transcription	Colon Smooth Muscle	Colon
27	chr13:40293400-40312600	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr13:40293600-40329000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
29	chr13:40294200-40339200	Weak transcription	Fetal Brain Male	brain
30	chr13:40294600-40327800	Weak transcription	NH-A	brain
31	chr13:40295600-40311200	Weak transcription	Spleen	Spleen
32	chr13:40295800-40308800	Weak transcription	HepG2	liver
33	chr13:40295800-40311000	Weak transcription	Pancreas	Pancrea
34	chr13:40296200-40311200	Weak transcription	Brain Angular Gyrus	brain
35	chr13:40296600-40312800	Weak transcription	Cortex derived primary cultured neurospheres	brain
36	chr13:40297600-40310800	Weak transcription	Primary T cells from cord blood	blood
37	chr13:40297600-40339800	Weak transcription	Brain Hippocampus Middle	brain
38	chr13:40297800-40309000	Weak transcription	Brain Substantia Nigra	brain
39	chr13:40297800-40310800	Weak transcription	Fetal Kidney	kidney
40	chr13:40297800-40310800	Weak transcription	Ovary	ovary
41	chr13:40297800-40313000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr13:40297800-40329800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr13:40298000-40310200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr13:40298000-40311400	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr13:40298400-40310200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr13:40298400-40311000	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr13:40298400-40311400	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr13:40298400-40314400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr13:40299200-40313000	Weak transcription	HMEC	breast
50	chr13:40299200-40327600	Weak transcription	Fetal Heart	heart

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