Variant report

Variant	rs7461545
Chromosome Location	chr8:99305363-99305364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:24719766..24721631-chr8:99304778..99307612,2	MCF-7	breast:
2	chr8:95651216..95652910-chr8:99304920..99307461,2	MCF-7	breast:
3	chr2:86421327..86423660-chr8:99303877..99305553,2	MCF-7	breast:
4	chr8:99268498..99270125-chr8:99304493..99306016,2	MCF-7	breast:
5	chr8:99304071..99306084-chr8:99410525..99412832,2	MCF-7	breast:
6	chr6:26204334..26206803-chr8:99304596..99307549,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000273080	Chromatin interaction
ENSG00000261437	Chromatin interaction
ENSG00000132305	Chromatin interaction
ENSG00000112308	Chromatin interaction
ENSG00000198518	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10103296	1.00[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes]
rs16896856	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17367639	1.00[CHD][hapmap]
rs4288343	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56110415	1.00[ASN][1000 genomes]
rs7010064	1.00[JPT][hapmap]
rs72664850	1.00[ASN][1000 genomes]
rs7819047	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7819152	1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7831149	1.00[JPT][hapmap]
rs7836665	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1032904	chr8:98756076-99476925	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	nsv539687	chr8:98756076-99476925	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
3	nsv831406	chr8:99290745-99482076	Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7461545	NIPAL2	cis	Whole Blood	GTEx
rs7461545	NIPAL2	cis	lymphoblastoid	seeQTL
rs7461545	NPAL2	cis	multi-tissue	Pritchard

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:99290800-99305400	Weak transcription	Aorta	Aorta
2	chr8:99291400-99305400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr8:99294800-99305400	Weak transcription	Right Atrium	heart
4	chr8:99296400-99305400	Weak transcription	Ovary	ovary
5	chr8:99296400-99305600	Weak transcription	Left Ventricle	heart
6	chr8:99296400-99305600	Weak transcription	Lung	lung
7	chr8:99296400-99305600	Weak transcription	Pancreas	Pancrea
8	chr8:99297800-99305400	Weak transcription	Esophagus	oesophagus
9	chr8:99298400-99305400	Weak transcription	Primary B cells from peripheral blood	blood
10	chr8:99302400-99305400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr8:99304000-99305400	Enhancers	Liver	Liver
12	chr8:99304200-99307400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr8:99304400-99305400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr8:99304400-99305400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr8:99304400-99305400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr8:99304400-99305400	Weak transcription	Stomach Mucosa	stomach
17	chr8:99304600-99305400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr8:99304600-99305400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr8:99304600-99305800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr8:99304600-99306000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr8:99304600-99306600	Active TSS	GM12878-XiMat	blood
22	chr8:99304600-99307400	Active TSS	Brain Anterior Caudate	brain
23	chr8:99304800-99305600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr8:99304800-99306400	Active TSS	NHLF	lung
25	chr8:99304800-99306800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:99304800-99306800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr8:99304800-99306800	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr8:99304800-99307000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr8:99304800-99312400	Weak transcription	K562	blood
30	chr8:99305000-99305400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr8:99305000-99305400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr8:99305000-99305400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr8:99305000-99305800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr8:99305000-99306200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr8:99305000-99306200	Flanking Active TSS	HUVEC	blood vessel
36	chr8:99305000-99306600	Active TSS	HMEC	breast
37	chr8:99305000-99306600	Active TSS	NHDF-Ad	bronchial
38	chr8:99305200-99305400	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
39	chr8:99305200-99305400	Bivalent Enhancer	Primary B cells from cord blood	blood
40	chr8:99305200-99305400	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr8:99305200-99305400	Flanking Active TSS	Fetal Heart	heart
42	chr8:99305200-99305400	Weak transcription	Fetal Intestine Small	intestine
43	chr8:99305200-99305400	Active TSS	Fetal Lung	lung
44	chr8:99305200-99305400	Enhancers	A549	lung
45	chr8:99305200-99305400	Flanking Active TSS	HepG2	liver
46	chr8:99305200-99305400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
47	chr8:99305200-99305600	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr8:99305200-99305800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr8:99305200-99305800	Flanking Active TSS	Osteobl	bone
50	chr8:99305200-99306000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

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