Variant report

Variant	rs4802747
Chromosome Location	chr19:39190588-39190589
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39188109..39192959-chr19:39197820..39200400,6	MCF-7	breast:
2	chr19:39152968..39155649-chr19:39189504..39191382,2	MCF-7	breast:
3	chr19:39189791..39192031-chr19:39202045..39204236,3	MCF-7	breast:
4	chr19:39135966..39142009-chr19:39184894..39201240,23	MCF-7	breast:
5	chr19:39150956..39153225-chr19:39190082..39192763,2	MCF-7	breast:
6	chr19:39188478..39190960-chr19:39339762..39341855,2	MCF-7	breast:
7	chr19:39165622..39167893-chr19:39189221..39191148,2	K562	blood:
8	chr19:39175021..39177149-chr19:39188221..39190892,2	MCF-7	breast:
9	chr19:39190500..39193880-chr19:39198148..39201069,3	MCF-7	breast:
10	chr19:39126238..39128898-chr19:39190173..39192471,2	K562	blood:
11	chr19:39185846..39187379-chr19:39189752..39191366,2	K562	blood:
12	chr19:39166875..39169119-chr19:39190078..39191942,2	MCF-7	breast:
13	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:
14	chr19:39173031..39174983-chr19:39187946..39191555,3	MCF-7	breast:
15	chr19:39188988..39191568-chr19:39196773..39198284,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000130402	Chromatin interaction
ENSG00000104824	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs11553600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052046	0.84[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];1.00[ASN][1000 genomes]
rs17589415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17665451	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41482151	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.82[LWK][hapmap];0.90[MEX][hapmap];0.95[MKK][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45468197	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616403	1.00[ASN][1000 genomes]
rs4801859	0.84[CEU][hapmap]
rs4802744	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4802775	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67438539	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67953948	1.00[ASN][1000 genomes]
rs7258742	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73032668	1.00[ASN][1000 genomes]
rs73032691	1.00[ASN][1000 genomes]
rs73032697	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73034621	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038909	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038918	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038924	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038930	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038932	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73038936	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73038948	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7351086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.90[MEX][hapmap];0.92[MKK][hapmap];0.92[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8103824	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8182484	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs888995	0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[MKK][hapmap];1.00[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	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
6	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4802747	ZNF526	cis	cerebellum	SCAN
rs4802747	TMEM145	cis	parietal	SCAN
rs4802747	KCNK6	cis	lymphoblastoid	seeQTL
rs4802747	ATP1A3	cis	parietal	SCAN
rs4802747	CAPN12	cis	lymphoblastoid	seeQTL
rs4802747	LYPD3	cis	cerebellum	SCAN
rs4802747	B9D2	cis	parietal	SCAN
rs4802747	CAPN12	cis	multi-tissue	Pritchard
rs4802747	RABAC1	cis	parietal	SCAN

Chromatin state (count:126 , 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	chr19:39179600-39205800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr19:39180000-39191600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr19:39180000-39192400	Genic enhancers	Lung	lung
8	chr19:39182000-39194200	Genic enhancers	Fetal Muscle Leg	muscle
9	chr19:39182200-39192600	Enhancers	Liver	Liver
10	chr19:39182200-39193400	Enhancers	Right Atrium	heart
11	chr19:39182200-39193800	Genic enhancers	Fetal Stomach	stomach
12	chr19:39182200-39214200	Genic enhancers	Fetal Muscle Trunk	muscle
13	chr19:39182200-39225200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr19:39182400-39193600	Genic enhancers	Esophagus	oesophagus
15	chr19:39182600-39190800	Genic enhancers	HepG2	liver
16	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
17	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
18	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
19	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
20	chr19:39184800-39190800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr19:39184800-39205800	Genic enhancers	A549	lung
22	chr19:39185000-39193600	Genic enhancers	HSMM	muscle
23	chr19:39185200-39205800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr19:39185400-39192000	Strong transcription	Osteobl	bone
25	chr19:39185800-39192600	Genic enhancers	Gastric	stomach
26	chr19:39186400-39190800	Weak transcription	Primary T helper cells PMA-I stimulated	--
27	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr19:39187000-39190600	Weak transcription	Primary B cells from cord blood	blood
29	chr19:39187000-39192400	Genic enhancers	Rectal Mucosa Donor 29	rectum
30	chr19:39187000-39196600	Weak transcription	Psoas Muscle	Psoas
31	chr19:39187200-39194600	Genic enhancers	Brain Inferior Temporal Lobe	brain
32	chr19:39187200-39195000	Genic enhancers	Pancreas	Pancrea
33	chr19:39187200-39201200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
34	chr19:39187200-39205800	Genic enhancers	Right Ventricle	heart
35	chr19:39187400-39190800	Weak transcription	Hela-S3	cervix
36	chr19:39187400-39191400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
37	chr19:39187600-39190600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr19:39187600-39190800	Weak transcription	Small Intestine	intestine
39	chr19:39187800-39190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr19:39187800-39195000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr19:39187800-39198600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr19:39188000-39190600	Enhancers	Adipose Nuclei	Adipose
43	chr19:39188000-39190600	Weak transcription	K562	blood
44	chr19:39188200-39190600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
45	chr19:39188200-39191000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr19:39188200-39191000	Enhancers	Stomach Mucosa	stomach
47	chr19:39188200-39191600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr19:39188200-39193400	Enhancers	Ovary	ovary
49	chr19:39188400-39190600	Enhancers	Fetal Thymus	thymus
50	chr19:39188400-39191000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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