Variant report

Variant	rs9548870
Chromosome Location	chr13:40231294-40231295
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	chr13:40229934..40232193-chr13:40232512..40234424,2	K562	blood:
2	chr13:40229027..40231888-chr13:40233465..40236904,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133103	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs3812882	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812883	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812884	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812885	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812886	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812887	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3812888	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4278626	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4312180	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4384490	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4415900	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941936	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941937	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941938	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4941939	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4941941	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943686	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4943687	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4943691	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6563732	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs67976778	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7327779	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7332791	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7335799	0.87[ASN][1000 genomes]
rs7984958	0.82[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9315725	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9532410	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532411	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9532412	0.96[ASN][1000 genomes]
rs9532413	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532414	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532420	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548865	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548866	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548867	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548868	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548869	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548875	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548880	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548893	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9548894	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9548896	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9566471	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9566472	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9576874	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576875	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576881	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9576882	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9548870	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9548870	COG6	cis	Muscle Skeletal	GTEx

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:40229400-40231400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr13:40229600-40231600	Active TSS	Pancreas	Pancrea
3	chr13:40230400-40231400	Flanking Active TSS	Dnd41	blood
4	chr13:40230600-40232000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr13:40230600-40234400	Weak transcription	Placenta	Placenta
6	chr13:40230600-40252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr13:40230600-40254600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:40230600-40254600	Weak transcription	Lung	lung
9	chr13:40230600-40254800	Weak transcription	Aorta	Aorta
10	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
11	chr13:40230800-40231400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr13:40230800-40231400	Enhancers	Small Intestine	intestine
13	chr13:40230800-40231600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr13:40230800-40231600	Enhancers	Primary B cells from peripheral blood	blood
15	chr13:40230800-40231600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr13:40230800-40231600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr13:40230800-40231800	Enhancers	Primary T cells fromperipheralblood	blood
18	chr13:40230800-40232000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr13:40230800-40232000	Enhancers	Primary T helper naive cells from peripheral blood	blood
20	chr13:40230800-40232200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr13:40230800-40232200	Enhancers	Colon Smooth Muscle	Colon
22	chr13:40230800-40232400	Weak transcription	Ovary	ovary
23	chr13:40230800-40233000	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr13:40230800-40234200	Weak transcription	Fetal Muscle Trunk	muscle
25	chr13:40230800-40235400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr13:40230800-40236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:40230800-40236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr13:40230800-40236200	Weak transcription	Fetal Intestine Small	intestine
29	chr13:40230800-40238800	Weak transcription	Fetal Kidney	kidney
30	chr13:40230800-40238800	Weak transcription	HSMM	muscle
31	chr13:40230800-40239400	Weak transcription	HSMMtube	muscle
32	chr13:40230800-40239600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr13:40230800-40239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr13:40230800-40240000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr13:40230800-40246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
37	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
38	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
39	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
41	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
42	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
43	chr13:40231000-40231400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr13:40231000-40231400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr13:40231000-40231400	Enhancers	Duodenum Mucosa	Duodenum
46	chr13:40231000-40231400	Weak transcription	Fetal Brain Male	brain
47	chr13:40231000-40231400	Enhancers	Fetal Muscle Leg	muscle
48	chr13:40231000-40231600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr13:40231000-40231600	Enhancers	GM12878-XiMat	blood
50	chr13:40231000-40232000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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