Variant report

Variant	rs11084108
Chromosome Location	chr19:52190559-52190560
allele	A/C
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:5)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr19:52176167..52177672-chr19:52190052..52191714,2	MCF-7	breast:
2	chr19:52163388..52165647-chr19:52189785..52191588,2	MCF-7	breast:
3	chr19:52189832..52192322-chr19:52204625..52207481,2	K562	blood:
4	chr19:52166500..52170915-chr19:52189684..52193816,5	MCF-7	breast:
5	chr19:52189901..52192880-chr19:52273718..52275861,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-HAS1-1	chr19:52190491-52192335	NONHSAT067461

No data

Variant related genes	Relation type
ENSG00000182310	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758504	chr19:51991896-52266700	Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	542 gene(s)	inside rSNPs	diseases
2	esv2758767	chr19:51991896-52604625	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	578 gene(s)	inside rSNPs	diseases
3	nsv482909	chr19:52091735-52266700	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	533 gene(s)	inside rSNPs	diseases
4	nsv1064914	chr19:52103914-52231564	Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	529 gene(s)	inside rSNPs	diseases
5	nsv544052	chr19:52103914-52271247	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	531 gene(s)	inside rSNPs	diseases
6	nsv1056825	chr19:52103914-52359815	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
7	nsv544053	chr19:52103914-52359815	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
8	nsv1065410	chr19:52103914-52889530	Genic enhancers Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	596 gene(s)	inside rSNPs	diseases
9	esv1843680	chr19:52131510-52211749	Active TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
10	nsv1066046	chr19:52147399-52271247	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
11	nsv544054	chr19:52147399-52271247	Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	525 gene(s)	inside rSNPs	diseases
12	nsv912296	chr19:52182363-52231032	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	518 gene(s)	inside rSNPs	diseases
13	nsv915725	chr19:52184488-52439676	Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	541 gene(s)	inside rSNPs	diseases
14	nsv9742	chr19:52187538-52221742	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	517 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11084108	ZNF784	cis	cerebellum	SCAN
rs11084108	NLRP11	cis	parietal	SCAN
rs11084108	ZSCAN5A	cis	parietal	SCAN
rs11084108	CHMP2A	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52184800-52190800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:52184800-52190800	Weak transcription	Right Atrium	heart
3	chr19:52185200-52190800	Weak transcription	Fetal Kidney	kidney
4	chr19:52185400-52190800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:52187600-52191000	Weak transcription	Psoas Muscle	Psoas
6	chr19:52189200-52190600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr19:52189200-52190800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr19:52189200-52190800	Enhancers	NHDF-Ad	bronchial
9	chr19:52189200-52190800	Enhancers	Osteobl	bone
10	chr19:52189400-52190600	Enhancers	HMEC	breast
11	chr19:52189400-52190600	Enhancers	NHLF	lung
12	chr19:52189400-52190800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr19:52189400-52190800	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr19:52189400-52190800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr19:52189400-52190800	Enhancers	HSMM	muscle
16	chr19:52189400-52191000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr19:52189600-52190600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr19:52189600-52190600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr19:52189600-52190800	Enhancers	Placenta Amnion	Placenta Amnion
20	chr19:52189800-52190800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr19:52189800-52190800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:52189800-52190800	Enhancers	Brain Germinal Matrix	brain
23	chr19:52189800-52190800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr19:52189800-52190800	Weak transcription	Left Ventricle	heart
25	chr19:52189800-52190800	Weak transcription	Right Ventricle	heart
26	chr19:52189800-52190800	Weak transcription	HSMMtube	muscle
27	chr19:52189800-52190800	Weak transcription	NHEK	skin
28	chr19:52189800-52191000	Weak transcription	Esophagus	oesophagus
29	chr19:52189800-52191000	Flanking Active TSS	A549	lung
30	chr19:52189800-52191000	Weak transcription	NH-A	brain
31	chr19:52190000-52190800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:52190000-52190800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr19:52190000-52190800	Enhancers	Stomach Smooth Muscle	stomach
34	chr19:52190000-52191000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr19:52190200-52190600	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr19:52190200-52190600	Enhancers	Duodenum Smooth Muscle	Duodenum
37	chr19:52190200-52190800	Enhancers	Fetal Brain Male	brain
38	chr19:52190200-52190800	Enhancers	Fetal Heart	heart
39	chr19:52190200-52190800	Enhancers	Fetal Lung	lung
40	chr19:52190200-52190800	Enhancers	Fetal Muscle Leg	muscle
41	chr19:52190200-52190800	Enhancers	Placenta	Placenta
42	chr19:52190200-52190800	Enhancers	K562	blood
43	chr19:52190200-52191200	Enhancers	Lung	lung
44	chr19:52190400-52190600	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr19:52190400-52190600	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr19:52190400-52190600	Flanking Active TSS	Hela-S3	cervix
47	chr19:52190400-52190800	Enhancers	H1 Cell Line	embryonic stem cell
48	chr19:52190400-52190800	Enhancers	H9 Cell Line	embryonic stem cell
49	chr19:52190400-52190800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr19:52190400-52190800	Enhancers	HUES64 Cell Line	embryonic stem cell

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