Variant report

Variant	rs2080988
Chromosome Location	chr19:39185557-39185558
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39185416-39185866	K562	blood:	n/a	n/a
2	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
3	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a

No data

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

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	chr19:39183521..39187102-chr19:39327849..39329398,3	MCF-7	breast:
4	chr19:39184301..39186024-chr19:39197035..39198967,2	K562	blood:
5	chr19:39184438..39186099-chr19:39190948..39193871,2	MCF-7	breast:

No data

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

Extended variants
information (count: 37 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1031849	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421863	0.90[AMR][1000 genomes]
rs10424568	0.80[ASN][1000 genomes]
rs1060186	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11083476	0.87[AMR][1000 genomes]
rs11665964	0.93[ASN][1000 genomes]
rs11672576	0.90[AMR][1000 genomes]
rs12462503	0.83[ASN][1000 genomes]
rs12984247	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1564203	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985636	0.84[ASN][1000 genomes]
rs2112649	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112651	0.82[ASN][1000 genomes]
rs3786841	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786843	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347742	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619518	0.90[AMR][1000 genomes]
rs4801861	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802797	0.81[AMR][1000 genomes]
rs6508813	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508814	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7249585	0.90[AMR][1000 genomes]
rs7252630	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749701	0.96[ASN][1000 genomes]
rs752067	0.83[ASN][1000 genomes]
rs755690	0.92[ASN][1000 genomes]
rs8099948	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107877	0.90[AMR][1000 genomes]
rs888996	0.82[ASN][1000 genomes]
rs888997	0.81[EUR][1000 genomes];0.81[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
rs2080988	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs2080988	CAPN12	cis	Adipose Subcutaneous	GTEx
rs2080988	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs2080988	CAPN12	cis	Esophagus Muscularis	GTEx
rs2080988	CAPN12	cis	Muscle Skeletal	GTEx
rs2080988	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	chr19:39180000-39186000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:39180000-39192400	Genic enhancers	Lung	lung
11	chr19:39180800-39187000	Enhancers	Primary T cells fromperipheralblood	blood
12	chr19:39181000-39186600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr19:39181400-39186800	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr19:39181800-39186400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr19:39182000-39185600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
17	chr19:39182200-39187800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr19:39182200-39192600	Enhancers	Liver	Liver
19	chr19:39182200-39193400	Enhancers	Right Atrium	heart
20	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
21	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
22	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr19:39182400-39186000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:39182400-39186600	Enhancers	Primary hematopoietic stem cells	blood
25	chr19:39182400-39187000	Enhancers	Stomach Mucosa	stomach
26	chr19:39182400-39189600	Enhancers	Brain Angular Gyrus	brain
27	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
28	chr19:39182600-39185600	Genic enhancers	Spleen	Spleen
29	chr19:39182600-39185800	Enhancers	Primary B cells from peripheral blood	blood
30	chr19:39182600-39185800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr19:39182600-39186000	Enhancers	Fetal Thymus	thymus
32	chr19:39182600-39186200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:39182600-39186400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr19:39182600-39186600	Genic enhancers	Sigmoid Colon	Sigmoid Colon
35	chr19:39182600-39186800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
36	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
37	chr19:39182600-39190800	Genic enhancers	HepG2	liver
38	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:39182800-39186000	Enhancers	H1 Cell Line	embryonic stem cell
40	chr19:39182800-39186000	Enhancers	H9 Cell Line	embryonic stem cell
41	chr19:39182800-39186400	Enhancers	Primary T cells from cord blood	blood
42	chr19:39183000-39185600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr19:39183000-39185800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr19:39183000-39186200	Enhancers	Fetal Kidney	kidney
45	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
46	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
47	chr19:39183200-39188800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
48	chr19:39183400-39186000	Genic enhancers	NHLF	lung
49	chr19:39183400-39187000	Enhancers	Primary B cells from cord blood	blood
50	chr19:39183400-39187600	Enhancers	Small Intestine	intestine

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