Variant report

Variant	rs7259861
Chromosome Location	chr19:52160743-52160744
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:51975913..51977254-chr19:52159906..52161263,12	MCF-7	breast:
2	chr19:52160347..52160857-chr19:52281258..52281779,2	K562	blood:
3	chr19:52110839..52111869-chr19:52159924..52160844,8	MCF-7	breast:
4	chr19:51975890..51976812-chr19:52159933..52160756,4	K562	blood:
5	chr19:52110880..52111497-chr19:52159833..52160812,2	MCF-7	breast:
6	chr19:52160319..52160911-chr19:52311474..52312517,3	K562	blood:
7	chr19:52159931..52161750-chr19:52173076..52176072,2	K562	blood:
8	chr19:51924885..51925819-chr19:52159862..52160853,7	K562	blood:

No data

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11883221	1.00[CHB][hapmap]
rs12459542	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16982907	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16982912	1.00[ASN][1000 genomes]
rs2902888	1.00[CHB][hapmap]
rs6417160	1.00[ASN][1000 genomes]
rs7250849	0.81[EUR][1000 genomes]
rs7255319	1.00[CHB][hapmap]
rs73052830	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052857	1.00[ASN][1000 genomes]
rs73052859	1.00[ASN][1000 genomes]
rs73052861	1.00[ASN][1000 genomes]
rs73052877	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv2532	chr19:52109105-52186946	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	nsv181	chr19:52113123-52162533	Strong transcription Enhancers Flanking Active TSS Genic enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv432071	chr19:52127053-52182363	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	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
13	nsv1065199	chr19:52142340-52165439	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv2757698	chr19:52142631-52165127	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	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
16	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7259861	SIGLEC14	cis	Nerve Tibial	GTEx
rs7259861	SIGLEC14	cis	lung	GTEx
rs7259861	SIGLEC14	cis	Whole Blood	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:52160000-52160800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr19:52160000-52160800	Enhancers	Primary B cells from peripheral blood	blood
3	chr19:52160000-52160800	Enhancers	Ovary	ovary
4	chr19:52160000-52160800	Bivalent Enhancer	Dnd41	blood
5	chr19:52160000-52160800	Enhancers	HMEC	breast
6	chr19:52160000-52160800	Enhancers	K562	blood
7	chr19:52160000-52161000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr19:52160000-52161000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr19:52160000-52162200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr19:52160000-52162200	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr19:52160000-52162600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr19:52160200-52160800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:52160200-52160800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:52160200-52160800	Enhancers	A549	lung
15	chr19:52160400-52160800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr19:52160400-52160800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr19:52160400-52160800	Weak transcription	Primary B cells from cord blood	blood
18	chr19:52160400-52160800	Enhancers	Adipose Nuclei	Adipose
19	chr19:52160400-52160800	Enhancers	Brain Hippocampus Middle	brain
20	chr19:52160400-52160800	Enhancers	Brain Substantia Nigra	brain
21	chr19:52160400-52160800	Enhancers	Colon Smooth Muscle	Colon
22	chr19:52160400-52160800	Enhancers	Right Atrium	heart
23	chr19:52160400-52160800	Enhancers	GM12878-XiMat	blood
24	chr19:52160400-52160800	Enhancers	NHDF-Ad	bronchial
25	chr19:52160400-52160800	Enhancers	NHEK	skin
26	chr19:52160400-52160800	Enhancers	Osteobl	bone
27	chr19:52160400-52161000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr19:52160600-52161000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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