Variant report

Variant	rs3786843
Chromosome Location	chr19:39187385-39187386
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39186779-39187727	A549	lung:	n/a	n/a
2	POLR2A	chr19:39187250-39188056	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:39187158-39187734	HepG2	liver:	n/a	n/a
4	POLR2A	chr19:39187352-39187463	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr19:39186808-39187452	K562	blood:	n/a	n/a
6	POLR2A	chr19:39187308-39188098	K562	blood:	n/a	n/a
7	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39187240-39187609	GM12891	blood:	n/a	n/a
9	POLR2A	chr19:39187193-39187687	ECC-1	luminal epithelium:	n/a	n/a
10	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a
11	POLR2A	chr19:39187165-39187855	Hela-S3	cervix:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39147345..39151436-chr19:39186794..39189528,4	MCF-7	breast:
2	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
3	chr19:39182129..39185762-chr19:39186877..39189539,4	MCF-7	breast:
4	chr19:39185891..39187427-chr19:39211415..39213129,2	K562	blood:
5	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000267375	TF binding region
ENSG00000130402	Chromatin interaction
ENSG00000267375	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1031849	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10421863	0.88[AMR][1000 genomes]
rs10424568	0.82[ASN][1000 genomes]
rs1060186	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11083476	0.85[AMR][1000 genomes]
rs11665964	0.96[ASN][1000 genomes]
rs11672576	0.88[AMR][1000 genomes]
rs12462503	0.81[ASN][1000 genomes]
rs12984247	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1564203	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1985636	0.82[ASN][1000 genomes]
rs2080988	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112649	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112651	0.80[ASN][1000 genomes]
rs3786841	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4347742	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4619518	0.88[AMR][1000 genomes]
rs4801861	0.85[EUR][1000 genomes]
rs4802743	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6508813	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6508814	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7249585	0.88[AMR][1000 genomes]
rs7252630	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs749701	0.99[ASN][1000 genomes]
rs752067	0.81[ASN][1000 genomes]
rs755690	0.94[ASN][1000 genomes]
rs8099948	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8107877	0.88[AMR][1000 genomes]
rs888996	0.80[ASN][1000 genomes]
rs888997	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs936524	0.88[AMR][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	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3786843	CAPN12	cis	Esophagus Muscularis	GTEx
rs3786843	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs3786843	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs3786843	CAPN12	cis	Adipose Subcutaneous	GTEx
rs3786843	CAPN12	cis	Heart Left Ventricle	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39164400-39200200	Genic enhancers	Fetal Intestine Small	intestine
2	chr19:39177200-39195000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:39178600-39187800	Enhancers	Left Ventricle	heart
4	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
5	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
6	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:39180000-39192400	Genic enhancers	Lung	lung
10	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
11	chr19:39182200-39187800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr19:39182200-39192600	Enhancers	Liver	Liver
13	chr19:39182200-39193400	Enhancers	Right Atrium	heart
14	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
15	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr19:39182400-39189600	Enhancers	Brain Angular Gyrus	brain
18	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
19	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
20	chr19:39182600-39190800	Genic enhancers	HepG2	liver
21	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
22	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
23	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
24	chr19:39183200-39188800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
25	chr19:39183400-39187600	Enhancers	Small Intestine	intestine
26	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
27	chr19:39183800-39188200	Weak transcription	Fetal Brain Female	brain
28	chr19:39184200-39187800	Weak transcription	Fetal Brain Male	brain
29	chr19:39184400-39187600	Weak transcription	K562	blood
30	chr19:39184400-39189200	Weak transcription	Brain Germinal Matrix	brain
31	chr19:39184400-39190200	Enhancers	Brain Anterior Caudate	brain
32	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
33	chr19:39184600-39188800	Genic enhancers	NHEK	skin
34	chr19:39184800-39187800	Genic enhancers	HMEC	breast
35	chr19:39184800-39188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr19:39184800-39188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr19:39184800-39188600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr19:39184800-39188600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr19:39184800-39188800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr19:39184800-39189600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
41	chr19:39184800-39190000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr19:39184800-39190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr19:39184800-39190800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:39184800-39205800	Genic enhancers	A549	lung
45	chr19:39185000-39188200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:39185000-39193600	Genic enhancers	HSMM	muscle
47	chr19:39185200-39188000	Genic enhancers	Adipose Nuclei	Adipose
48	chr19:39185200-39188200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr19:39185200-39188400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr19:39185200-39188400	Strong transcription	Dnd41	blood

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