Variant report

Variant	rs4802743
Chromosome Location	chr19:39188064-39188065
allele	C/G
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	MYC	chr19:39187869-39188159	MCF10A-Er-Src	breast:	n/a	chr19:39187978-39187993 chr19:39187981-39187992 chr19:39187982-39187991 chr19:39187980-39187995
2	POLR2A	chr19:39187934-39188096	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr19:39187878-39188799	U87	brain:	n/a	n/a
4	POLR2A	chr19:39187972-39189382	A549	lung:	n/a	n/a
5	FOS	chr19:39187872-39188142	MCF10A-Er-Src	breast:	n/a	n/a
6	POLR2A	chr19:39187884-39188798	U87	brain:	n/a	n/a
7	POLR2A	chr19:39187308-39188098	K562	blood:	n/a	n/a
8	POLR2A	chr19:39164600-39206677	PANC-1	pancreas:	n/a	n/a
9	FOS	chr19:39187869-39188128	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr19:39187886-39188149	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr19:39164601-39206634	PANC-1	pancreas:	n/a	n/a
12	MYC	chr19:39187871-39188173	MCF10A-Er-Src	breast:	n/a	chr19:39187978-39187993 chr19:39187981-39187992 chr19:39187982-39187991 chr19:39187980-39187995

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	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:
5	chr19:39173031..39174983-chr19:39187946..39191555,3	MCF-7	breast:

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

Extended variants
information (count: 39 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1031849	0.87[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10421863	0.90[CHB][hapmap];0.90[AMR][1000 genomes]
rs10424568	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs1060186	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11083476	0.87[AMR][1000 genomes]
rs11665964	0.91[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11672576	0.90[AMR][1000 genomes]
rs12462503	0.85[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[ASN][1000 genomes]
rs12984247	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1564203	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1985636	0.84[ASN][1000 genomes]
rs2080988	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2112651	0.82[ASN][1000 genomes]
rs3786841	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3786843	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347742	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4619518	0.90[AMR][1000 genomes]
rs4801861	0.94[CEU][hapmap];0.90[CHB][hapmap];0.87[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4802797	0.81[AMR][1000 genomes]
rs6508813	0.94[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6508814	0.98[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	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749701	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs752067	0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.83[ASN][1000 genomes]
rs755690	0.92[ASN][1000 genomes]
rs8099948	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8107877	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes]
rs888996	0.82[ASN][1000 genomes]
rs888997	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9304576	0.81[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs9304577	0.94[JPT][hapmap]
rs936524	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs4802743	CTD-2540F13.2	cis	Adipose Subcutaneous	GTEx
rs4802743	CTD-2540F13.2	cis	Nerve Tibial	GTEx
rs4802743	CAPN12	cis	Muscle Skeletal	GTEx
rs4802743	CAPN12	cis	Esophagus Muscularis	GTEx
rs4802743	CAPN12	cis	Heart Left Ventricle	GTEx
rs4802743	CAPN12	cis	Adipose Subcutaneous	GTEx
rs4802743	CAPN12	cis	multi-tissue	Pritchard

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	chr19:39178600-39190600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr19:39178600-39198200	Genic enhancers	Fetal Intestine Large	intestine
5	chr19:39179000-39189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr19:39180000-39192400	Genic enhancers	Lung	lung
9	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
10	chr19:39182200-39192600	Enhancers	Liver	Liver
11	chr19:39182200-39193400	Enhancers	Right Atrium	heart
12	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
13	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
14	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr19:39182400-39189600	Enhancers	Brain Angular Gyrus	brain
16	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
17	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
18	chr19:39182600-39190800	Genic enhancers	HepG2	liver
19	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
20	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
21	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
22	chr19:39183200-39188800	Genic enhancers	Duodenum Smooth Muscle	Duodenum
23	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
24	chr19:39183800-39188200	Weak transcription	Fetal Brain Female	brain
25	chr19:39184400-39189200	Weak transcription	Brain Germinal Matrix	brain
26	chr19:39184400-39190200	Enhancers	Brain Anterior Caudate	brain
27	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
28	chr19:39184600-39188800	Genic enhancers	NHEK	skin
29	chr19:39184800-39188200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr19:39184800-39188600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr19:39184800-39188600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr19:39184800-39188600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr19:39184800-39188800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:39184800-39189600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr19:39184800-39190000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr19:39184800-39190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr19:39184800-39190800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr19:39184800-39205800	Genic enhancers	A549	lung
39	chr19:39185000-39188200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr19:39185000-39193600	Genic enhancers	HSMM	muscle
41	chr19:39185200-39188200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr19:39185200-39188400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr19:39185200-39188400	Strong transcription	Dnd41	blood
44	chr19:39185200-39205800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr19:39185400-39192000	Strong transcription	Osteobl	bone
46	chr19:39185600-39189000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr19:39185800-39189600	Enhancers	Brain Substantia Nigra	brain
48	chr19:39185800-39189800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr19:39185800-39190000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr19:39185800-39190000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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