Variant report

Variant	rs6471520
Chromosome Location	chr8:96112703-96112704
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:96107778..96115564-chr8:96144421..96149353,22	MCF-7	breast:
2	chr8:96111950..96115004-chr8:96279819..96283605,3	MCF-7	breast:
3	chr8:96108471..96116302-chr8:96144708..96150629,15	MCF-7	breast:
4	chr8:96077629..96090166-chr8:96105796..96116852,50	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C8orf38-1	chr8:96112622-96112756	NONHSAT127824

Variant related genes	Relation type
ENSG00000175895	Chromatin interaction
ENSG00000245080	Chromatin interaction
ENSG00000156172	Chromatin interaction
ENSG00000253773	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12548426	0.87[TSI][hapmap]
rs1946944	0.84[TSI][hapmap]
rs4734298	0.84[TSI][hapmap]
rs6471521	0.92[CEU][hapmap];0.90[CHB][hapmap];0.81[JPT][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[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	nsv1017301	chr8:95273503-96248352	Weak transcription Enhancers Active TSS Flanking 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	87 gene(s)	inside rSNPs	diseases
2	nsv539680	chr8:95273503-96248352	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv508520	chr8:95939373-96140068	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv891205	chr8:96062601-96115476	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
5	nsv891206	chr8:96092251-96115476	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv891207	chr8:96106037-96160914	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6471520	LAPTM4B	cis	parietal	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:96100400-96113600	Weak transcription	Lung	lung
2	chr8:96107800-96113400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr8:96108200-96113400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr8:96111000-96113000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr8:96111400-96113400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr8:96111600-96112800	Enhancers	Fetal Intestine Small	intestine
7	chr8:96111600-96113200	Enhancers	Fetal Muscle Leg	muscle
8	chr8:96111600-96113800	Enhancers	Fetal Thymus	thymus
9	chr8:96111600-96113800	Enhancers	Pancreas	Pancrea
10	chr8:96111600-96114000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr8:96111600-96114200	Enhancers	Primary B cells from peripheral blood	blood
12	chr8:96111600-96114200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr8:96111600-96114600	Enhancers	HMEC	breast
14	chr8:96111800-96112800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr8:96111800-96112800	Enhancers	Colonic Mucosa	Colon
16	chr8:96111800-96112800	Enhancers	Fetal Stomach	stomach
17	chr8:96111800-96113600	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr8:96111800-96113800	Enhancers	Primary hematopoietic stem cells short term culture	blood
19	chr8:96111800-96114000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr8:96112000-96112800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr8:96112000-96112800	Enhancers	Muscle Satellite Cultured Cells	--
22	chr8:96112000-96112800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
23	chr8:96112000-96113000	Enhancers	Primary B cells from cord blood	blood
24	chr8:96112000-96113000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr8:96112000-96113000	Enhancers	Brain Hippocampus Middle	brain
26	chr8:96112000-96113000	Enhancers	Brain Substantia Nigra	brain
27	chr8:96112000-96113000	Active TSS	Duodenum Smooth Muscle	Duodenum
28	chr8:96112000-96113200	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr8:96112000-96113200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr8:96112000-96113400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr8:96112000-96113400	Enhancers	Colon Smooth Muscle	Colon
32	chr8:96112000-96113600	Enhancers	Placenta	Placenta
33	chr8:96112000-96113800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr8:96112000-96113800	Flanking Active TSS	HUVEC	blood vessel
35	chr8:96112000-96113800	Flanking Active TSS	NH-A	brain
36	chr8:96112000-96113800	Enhancers	NHDF-Ad	bronchial
37	chr8:96112000-96114400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr8:96112000-96114600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr8:96112200-96113000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
40	chr8:96112200-96113000	Weak transcription	Left Ventricle	heart
41	chr8:96112200-96113000	Flanking Active TSS	Dnd41	blood
42	chr8:96112200-96113000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
43	chr8:96112200-96113200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr8:96112200-96113200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr8:96112200-96113200	Flanking Active TSS	Fetal Kidney	kidney
46	chr8:96112200-96113400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
47	chr8:96112200-96113400	Flanking Active TSS	Liver	Liver
48	chr8:96112200-96113400	Flanking Active TSS	Duodenum Mucosa	Duodenum
49	chr8:96112200-96113400	Flanking Active TSS	NHEK	skin
50	chr8:96112200-96113600	Flanking Active TSS	GM12878-XiMat	blood

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