Variant report

Variant	rs7896883
Chromosome Location	chr10:98787354-98787355
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:98590990..98593899-chr10:98785293..98787590,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196233	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11188985	0.91[CHB][hapmap];0.88[CHD][hapmap];0.85[MEX][hapmap];0.81[ASN][1000 genomes]
rs2817672	0.83[EUR][1000 genomes]
rs7922865	0.82[TSI][hapmap]
rs9665344	0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[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	nsv532232	chr10:98360775-99141797	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv1052931	chr10:98676192-98862301	Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1042398	chr10:98691406-98851346	Enhancers Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7896883	LOXL4	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:98777600-98791000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr10:98778000-98797200	Strong transcription	Fetal Thymus	thymus
3	chr10:98778800-98794400	Weak transcription	Thymus	Thymus
4	chr10:98781200-98788400	Weak transcription	Brain Germinal Matrix	brain
5	chr10:98781200-98789600	Weak transcription	Brain Anterior Caudate	brain
6	chr10:98781200-98790400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr10:98781200-98790600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr10:98781200-98791800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr10:98781200-98792800	Weak transcription	Fetal Brain Male	brain
10	chr10:98781200-98794200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr10:98781200-98797000	Weak transcription	Gastric	stomach
12	chr10:98782000-98792400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr10:98782600-98789600	Weak transcription	Fetal Brain Female	brain
14	chr10:98784200-98797000	Weak transcription	Pancreas	Pancrea
15	chr10:98784200-98797400	Weak transcription	Esophagus	oesophagus
16	chr10:98784800-98788200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr10:98785200-98792200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr10:98785600-98797200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr10:98785800-98797000	Weak transcription	Brain Angular Gyrus	brain
20	chr10:98785800-98797000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr10:98785800-98797000	Weak transcription	Brain Substantia Nigra	brain

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