Variant report

Variant	rs9532413
Chromosome Location	chr13:40235679-40235680
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:40235362..40236092-chr14:53549695..53550409,2	MCF-7	breast:
2	chr13:40229027..40231888-chr13:40233465..40236904,4	MCF-7	breast:
3	chr13:40228867..40231362-chr13:40235168..40238124,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133103	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs3812882	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812883	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812884	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812885	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3812886	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812887	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3812888	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4278626	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4312180	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4384490	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4415900	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941936	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941937	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941938	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4941939	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941941	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4943686	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4943687	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4943691	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6563732	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67976778	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7325068	0.80[ASN][1000 genomes]
rs7327779	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7332791	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7335799	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984958	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9315725	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532410	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9532411	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9532412	0.95[ASN][1000 genomes]
rs9532414	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532420	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548865	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548866	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548867	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548868	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548869	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548870	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548875	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548880	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548893	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9548894	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9548896	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566471	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9566472	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9576874	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576875	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9576881	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9576882	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv870429	chr13:40235061-40265634	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region miRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9532413	COG6	Cis_1M	lymphoblastoid	RTeQTL
rs9532413	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	chr13:40230600-40252200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:40230600-40254600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr13:40230600-40254600	Weak transcription	Lung	lung
4	chr13:40230600-40254800	Weak transcription	Aorta	Aorta
5	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
6	chr13:40230800-40236000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr13:40230800-40236200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr13:40230800-40236200	Weak transcription	Fetal Intestine Small	intestine
9	chr13:40230800-40238800	Weak transcription	Fetal Kidney	kidney
10	chr13:40230800-40238800	Weak transcription	HSMM	muscle
11	chr13:40230800-40239400	Weak transcription	HSMMtube	muscle
12	chr13:40230800-40239600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr13:40230800-40239800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:40230800-40240000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr13:40230800-40246600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr13:40230800-40254600	Weak transcription	Left Ventricle	heart
17	chr13:40230800-40254600	Weak transcription	Psoas Muscle	Psoas
18	chr13:40230800-40254800	Weak transcription	Fetal Thymus	thymus
19	chr13:40230800-40256400	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr13:40230800-40258400	Weak transcription	Colonic Mucosa	Colon
21	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
22	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
23	chr13:40231000-40237800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr13:40231000-40238800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr13:40231000-40239200	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr13:40231000-40241600	Weak transcription	Hela-S3	cervix
27	chr13:40231000-40243800	Weak transcription	Fetal Heart	heart
28	chr13:40231000-40252200	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr13:40231000-40252800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr13:40231000-40254400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr13:40231000-40254400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr13:40231000-40254600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
33	chr13:40231000-40254600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr13:40231000-40254600	Weak transcription	NHLF	lung
35	chr13:40231000-40256400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr13:40231000-40256400	Weak transcription	NHEK	skin
37	chr13:40231000-40257200	Weak transcription	HMEC	breast
38	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
39	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
40	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr13:40231200-40236200	Weak transcription	K562	blood
43	chr13:40231200-40239600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr13:40231200-40254400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr13:40231200-40254600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:40231200-40254800	Weak transcription	Fetal Stomach	stomach
47	chr13:40231400-40237800	Weak transcription	Fetal Muscle Leg	muscle
48	chr13:40231400-40253600	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr13:40231400-40254600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus

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