Variant report

Variant	rs10104620
Chromosome Location	chr8:89216061-89216062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:89215336..89216269-chr8:89293539..89294172,2	MCF-7	breast:
2	chr8:89215266..89216237-chr8:89301663..89302377,6	MCF-7	breast:
3	chr8:89215240..89216267-chr8:89301694..89302670,5	MCF-7	breast:
4	chr8:89215742..89216325-chr8:89296713..89297368,2	MCF-7	breast:
5	chr8:89215614..89216190-chr8:89332907..89333555,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10091022	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10099839	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10110977	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10113080	0.94[EUR][1000 genomes]
rs13256568	0.94[EUR][1000 genomes]
rs13261169	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13264048	0.93[EUR][1000 genomes]
rs13439559	0.94[EUR][1000 genomes]
rs16879913	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16881281	0.93[CEU][hapmap]
rs28542805	0.81[ASN][1000 genomes]
rs28589951	0.81[ASN][1000 genomes]
rs28639477	0.81[ASN][1000 genomes]
rs28649468	0.94[EUR][1000 genomes]
rs28678551	0.94[EUR][1000 genomes]
rs28730305	0.81[ASN][1000 genomes]
rs28904614	0.94[EUR][1000 genomes]
rs28904635	1.00[ASN][1000 genomes]
rs6469298	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7357573	0.94[EUR][1000 genomes]
rs7357575	0.94[EUR][1000 genomes]
rs7357576	0.94[EUR][1000 genomes]
rs7821734	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs939280	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029898	chr8:88837956-89606641	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv1030028	chr8:89060085-89733470	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1019111	chr8:89186908-89475460	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831386	chr8:89209788-89403546	Enhancers Genic enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10104620	LOC338579	trans	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:89160800-89217200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr8:89177200-89216400	Weak transcription	Brain Germinal Matrix	brain
3	chr8:89195000-89219200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr8:89201200-89218000	Weak transcription	Fetal Lung	lung
5	chr8:89204000-89219600	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr8:89204200-89217200	Weak transcription	NH-A	brain
7	chr8:89208000-89217200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr8:89211600-89217000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr8:89211800-89217200	Weak transcription	Fetal Brain Female	brain
10	chr8:89212400-89217200	Weak transcription	Fetal Brain Male	brain
11	chr8:89212600-89216200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr8:89212600-89217000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr8:89212800-89217200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr8:89213000-89217000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr8:89214800-89219800	Weak transcription	Fetal Intestine Large	intestine
16	chr8:89215000-89217200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr8:89215200-89217200	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr8:89215200-89219400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr8:89215200-89227600	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr8:89215600-89219200	Enhancers	Pancreatic Islets	Pancreatic Islet
21	chr8:89215800-89218200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr8:89215800-89218200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr8:89216000-89216200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr8:89216000-89216600	Enhancers	Osteobl	bone
25	chr8:89216000-89217400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr8:89216000-89217400	Enhancers	Fetal Heart	heart

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