Variant report

Variant	rs749702
Chromosome Location	chr19:39189895-39189896
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 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	chr19:39188478..39190960-chr19:39339762..39341855,2	MCF-7	breast:
6	chr19:39165622..39167893-chr19:39189221..39191148,2	K562	blood:
7	chr19:39175021..39177149-chr19:39188221..39190892,2	MCF-7	breast:
8	chr19:39185846..39187379-chr19:39189752..39191366,2	K562	blood:
9	chr19:39176509..39181573-chr19:39186750..39192510,7	K562	blood:
10	chr19:39173031..39174983-chr19:39187946..39191555,3	MCF-7	breast:
11	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: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs2306197	0.91[ASN][1000 genomes]
rs3786838	0.94[ASN][1000 genomes]
rs3786844	0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs3786850	0.87[ASN][1000 genomes]
rs4801859	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs60580755	0.93[ASN][1000 genomes]
rs7246615	0.82[ASW][hapmap]

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
rs749702	ATP1A3	cis	parietal	SCAN
rs749702	CAPN12	cis	lymphoblastoid	seeQTL
rs749702	CAPN12	cis	multi-tissue	Pritchard
rs749702	TMEM145	cis	parietal	SCAN
rs749702	LYPD3	cis	cerebellum	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	chr19:39182600-39190200	Genic enhancers	Colonic Mucosa	Colon
16	chr19:39182600-39190800	Genic enhancers	HepG2	liver
17	chr19:39182600-39193800	Genic enhancers	Rectal Mucosa Donor 31	rectum
18	chr19:39183000-39190000	Enhancers	Brain Cingulate Gyrus	brain
19	chr19:39183000-39196600	Enhancers	Fetal Heart	heart
20	chr19:39183400-39191000	Genic enhancers	Placenta	Placenta
21	chr19:39184400-39190200	Enhancers	Brain Anterior Caudate	brain
22	chr19:39184400-39191200	Enhancers	Brain Hippocampus Middle	brain
23	chr19:39184800-39190000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:39184800-39190400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr19:39184800-39190800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr19:39184800-39205800	Genic enhancers	A549	lung
27	chr19:39185000-39193600	Genic enhancers	HSMM	muscle
28	chr19:39185200-39205800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr19:39185400-39192000	Strong transcription	Osteobl	bone
30	chr19:39185800-39190000	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr19:39185800-39190000	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:39185800-39192600	Genic enhancers	Gastric	stomach
33	chr19:39186000-39190000	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr19:39186000-39190400	Strong transcription	NHLF	lung
35	chr19:39186200-39190000	Genic enhancers	Rectal Smooth Muscle	rectum
36	chr19:39186400-39190000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr19:39186400-39190800	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr19:39186400-39213400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:39186800-39190000	Genic enhancers	Spleen	Spleen
40	chr19:39187000-39190600	Weak transcription	Primary B cells from cord blood	blood
41	chr19:39187000-39192400	Genic enhancers	Rectal Mucosa Donor 29	rectum
42	chr19:39187000-39196600	Weak transcription	Psoas Muscle	Psoas
43	chr19:39187200-39194600	Genic enhancers	Brain Inferior Temporal Lobe	brain
44	chr19:39187200-39195000	Genic enhancers	Pancreas	Pancrea
45	chr19:39187200-39201200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
46	chr19:39187200-39205800	Genic enhancers	Right Ventricle	heart
47	chr19:39187400-39190800	Weak transcription	Hela-S3	cervix
48	chr19:39187400-39191400	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
49	chr19:39187600-39190200	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr19:39187600-39190600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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