Variant report

Variant	rs4943691
Chromosome Location	chr13:40259490-40259491
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:40258206..40259608-chr13:41351110..41352030,5	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs3812882	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812883	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812884	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3812885	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812886	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812887	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3812888	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4278626	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4312180	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4384490	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4408422	0.81[ASN][1000 genomes]
rs4415900	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941936	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941937	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941938	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4941939	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4941941	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943686	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4943687	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6563732	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs67976778	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7325068	0.82[ASN][1000 genomes]
rs7327779	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7332791	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7335799	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7984958	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9315725	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532410	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9532411	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9532412	0.93[ASN][1000 genomes]
rs9532413	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532414	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9532420	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548865	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548866	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548867	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548868	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9548869	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9548870	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9548875	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548880	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548893	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9548894	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9548896	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566471	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9566472	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9576874	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9576875	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9576881	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9576882	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][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	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
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4943691	COG6	cis	Muscle Skeletal	GTEx
rs4943691	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	chr13:40230600-40263800	Weak transcription	Spleen	Spleen
2	chr13:40230800-40262000	Weak transcription	Thymus	Thymus
3	chr13:40230800-40275000	Weak transcription	Right Ventricle	heart
4	chr13:40231000-40261800	Weak transcription	Brain Substantia Nigra	brain
5	chr13:40231000-40266200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr13:40231000-40270800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr13:40231000-40286000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:40231400-40264200	Weak transcription	Esophagus	oesophagus
9	chr13:40231400-40268000	Weak transcription	Small Intestine	intestine
10	chr13:40231600-40270200	Weak transcription	Gastric	stomach
11	chr13:40233000-40273600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr13:40233000-40295600	Weak transcription	Pancreas	Pancrea
13	chr13:40236800-40261600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr13:40238000-40291600	Weak transcription	Fetal Intestine Small	intestine
15	chr13:40238600-40261600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr13:40241200-40261600	Weak transcription	HSMM	muscle
17	chr13:40246200-40262800	Weak transcription	Fetal Heart	heart
18	chr13:40246400-40297400	Weak transcription	HUVEC	blood vessel
19	chr13:40252200-40261800	Weak transcription	K562	blood
20	chr13:40253000-40266200	Weak transcription	Colon Smooth Muscle	Colon
21	chr13:40253400-40266600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr13:40254600-40264000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr13:40255000-40261800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr13:40255000-40261800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr13:40255000-40262400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr13:40255000-40262400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr13:40255000-40262400	Weak transcription	Aorta	Aorta
28	chr13:40255000-40263800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr13:40255000-40264200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr13:40255000-40266600	Weak transcription	Fetal Stomach	stomach
31	chr13:40255000-40268000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr13:40255000-40270000	Weak transcription	Lung	lung
33	chr13:40255000-40291200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr13:40255000-40306000	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr13:40255200-40261600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr13:40255200-40261800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr13:40255200-40262400	Weak transcription	HSMMtube	muscle
38	chr13:40255200-40265800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr13:40255200-40272800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr13:40255200-40291000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr13:40255400-40261200	Weak transcription	Fetal Brain Female	brain
42	chr13:40255400-40261600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr13:40255400-40261600	Weak transcription	NH-A	brain
44	chr13:40255400-40261800	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr13:40255400-40261800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr13:40255400-40262000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr13:40255400-40266800	Weak transcription	NHLF	lung
48	chr13:40255400-40272800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr13:40255600-40259600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
50	chr13:40255600-40261600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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