Variant report

Variant	rs905552
Chromosome Location	chr11:19096159-19096160
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:19094423..19096324-chr11:19165752..19167827,2	MCF-7	breast:
2	chr11:19092484..19094846-chr11:19096156..19098835,2	MCF-7	breast:
3	chr11:19093295..19097207-chr11:19260781..19264758,3	K562	blood:

Variant related genes	Relation type
ENSG00000129173	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs1011179	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10833054	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1125217	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12802650	0.85[CEU][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1393957	0.82[ASW][hapmap]
rs1503500	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7945401	0.81[EUR][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	nsv1040805	chr11:19037871-19892803	Enhancers Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	nsv540957	chr11:19037871-19892803	Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	nsv897030	chr11:19049478-19106045	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs905552	SAA3P	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:19093200-19096200	Enhancers	Gastric	stomach
2	chr11:19093400-19097000	Enhancers	Stomach Mucosa	stomach
3	chr11:19093400-19098200	Weak transcription	HUVEC	blood vessel
4	chr11:19093400-19098800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr11:19093600-19098800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr11:19094000-19096200	Enhancers	Pancreas	Pancrea
7	chr11:19094200-19096400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr11:19094800-19096200	Enhancers	iPS-15b Cell Line	embryonic stem cell
9	chr11:19094800-19096200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:19095000-19096200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr11:19095000-19096200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr11:19095000-19096200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr11:19095000-19096400	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr11:19095000-19096400	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr11:19095200-19101000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr11:19095200-19101000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:19095200-19104000	Weak transcription	Esophagus	oesophagus
18	chr11:19095400-19096400	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr11:19095600-19096200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr11:19095600-19096400	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr11:19095800-19096200	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr11:19095800-19098200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr11:19095800-19098800	Weak transcription	Adipose Nuclei	Adipose
24	chr11:19096000-19096400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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