Variant report

Variant	rs3786841
Chromosome Location	chr19:39186229-39186230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39185589-39186405	U87	brain:	n/a	n/a
2	EBF1	chr19:39185905-39186266	GM12878	blood:	n/a	n/a
3	SPI1	chr19:39185830-39186356	HL-60	blood:	n/a	chr19:39186126-39186133 chr19:39186120-39186133 chr19:39185934-39185947
4	POLR2A	chr19:39186125-39186357	HUVEC	blood vessel:	n/a	n/a
5	POLR2A	chr19:39185955-39186930	K562	blood:	n/a	n/a
6	POLR2A	chr19:39186141-39186365	MCF-7	breast:	n/a	n/a
7	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a
9	EP300	chr19:39186024-39187337	SK-N-SH	brain:	n/a	chr19:39186087-39186101

No.	Distal block	Cell Line	Cell type
1	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
2	chr19:39138523..39140203-chr19:39185373..39187199,2	MCF-7	breast:
3	chr19:39185846..39187379-chr19:39189752..39191366,2	K562	blood:
4	chr19:39183521..39187102-chr19:39327849..39329398,3	MCF-7	breast:
5	chr19:39185891..39187427-chr19:39211415..39213129,2	K562	blood:

Variant related genes	Relation type
ENSG00000267375	TF binding region
ENSG00000104824	Chromatin interaction
ENSG00000130402	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs1031849	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10421863	0.90[AMR][1000 genomes]
rs1060186	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11083476	0.87[AMR][1000 genomes]
rs11665964	0.93[ASN][1000 genomes]
rs11672576	0.90[AMR][1000 genomes]
rs12462503	0.82[ASN][1000 genomes]
rs12984247	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1564203	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985636	0.83[ASN][1000 genomes]
rs2080988	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112649	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2112651	0.81[ASN][1000 genomes]
rs3786843	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4347742	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4619518	0.90[AMR][1000 genomes]
rs4801861	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802743	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4802797	0.81[AMR][1000 genomes]
rs6508813	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6508814	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7249585	0.90[AMR][1000 genomes]
rs7252630	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs749701	0.96[ASN][1000 genomes]
rs752067	0.82[ASN][1000 genomes]
rs755690	0.91[ASN][1000 genomes]
rs8099948	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8107877	0.90[AMR][1000 genomes]
rs888996	0.81[ASN][1000 genomes]
rs888997	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs936524	0.90[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3786841	CAPN12	cis	Muscle Skeletal	GTEx
rs3786841	CAPN12	cis	Heart Left Ventricle	GTEx
rs3786841	CAPN12	cis	Esophagus Muscularis	GTEx
rs3786841	CAPN12	cis	Adipose Subcutaneous	GTEx
rs3786841	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs3786841	CTD-2540F13.2	cis	Adipose Subcutaneous	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	chr19:39180800-39187000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr19:39181000-39186600	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr19:39181400-39186800	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr19:39181800-39186400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
15	chr19:39182200-39187800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:39182200-39192600	Enhancers	Liver	Liver
17	chr19:39182200-39193400	Enhancers	Right Atrium	heart
18	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
19	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
20	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr19:39182400-39186600	Enhancers	Primary hematopoietic stem cells	blood
22	chr19:39182400-39187000	Enhancers	Stomach Mucosa	stomach
23	chr19:39182400-39189600	Enhancers	Brain Angular Gyrus	brain
24	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
25	chr19:39182600-39186400	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr19:39182600-39186600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
27	chr19:39182600-39186800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
28	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
29	chr19:39182600-39190800	Genic enhancers	HepG2	liver
30	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
31	chr19:39182800-39186400	Enhancers	Primary T cells from cord blood	blood
32	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
33	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
34	chr19:39183200-39188800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
35	chr19:39183400-39187000	Enhancers	Primary B cells from cord blood	blood
36	chr19:39183400-39187600	Enhancers	Small Intestine	intestine
37	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
38	chr19:39183800-39188200	Weak transcription	Fetal Brain Female	brain
39	chr19:39184000-39187200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr19:39184200-39186400	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr19:39184200-39187800	Weak transcription	Fetal Brain Male	brain
42	chr19:39184400-39187200	Enhancers	Brain Inferior Temporal Lobe	brain
43	chr19:39184400-39187600	Weak transcription	K562	blood
44	chr19:39184400-39189200	Weak transcription	Brain Germinal Matrix	brain
45	chr19:39184400-39190200	Enhancers	Brain Anterior Caudate	brain
46	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
47	chr19:39184600-39186400	Genic enhancers	Muscle Satellite Cultured Cells	--
48	chr19:39184600-39186600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
49	chr19:39184600-39187200	Enhancers	Right Ventricle	heart
50	chr19:39184600-39188800	Genic enhancers	NHEK	skin

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