Variant report

Variant	rs10838725
Chromosome Location	chr11:47557871-47557872
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47556312..47559007-chr11:47559496..47562082,2	MCF-7	breast:
2	chr11:47556504..47558457-chr11:47638712..47641328,2	K562	blood:
3	chr11:47544419..47546383-chr11:47555252..47558176,2	MCF-7	breast:
4	chr11:47557144..47558701-chr11:47561698..47563428,2	K562	blood:
5	chr11:47556325..47561893-chr11:47562676..47568878,7	K562	blood:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10742814	0.82[ASN][1000 genomes]
rs10838726	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838731	0.88[AMR][1000 genomes]
rs11039280	0.85[ASN][1000 genomes]
rs11039284	0.80[AMR][1000 genomes]
rs11039290	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11039297	0.82[AMR][1000 genomes]
rs11039332	0.80[AMR][1000 genomes]
rs12365079	0.80[AMR][1000 genomes]
rs12577643	0.81[ASN][1000 genomes]
rs61895112	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6485758	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7103648	0.82[ASN][1000 genomes]
rs7104036	0.82[ASN][1000 genomes]
rs7120548	0.82[AMR][1000 genomes]
rs71475921	0.94[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7933019	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[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	nsv897325	chr11:47411736-47600438	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1036011	chr11:47413060-47582279	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Alzheimer's disease (late onset)	24162737	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10838725	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47546000-47572400	Weak transcription	Fetal Intestine Large	intestine
2	chr11:47546200-47560400	Weak transcription	Esophagus	oesophagus
3	chr11:47546400-47558000	Weak transcription	Fetal Lung	lung
4	chr11:47546400-47560400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr11:47546400-47560800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr11:47546400-47561200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr11:47546400-47564200	Weak transcription	Thymus	Thymus
8	chr11:47546400-47573400	Weak transcription	Colonic Mucosa	Colon
9	chr11:47546400-47573600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr11:47546600-47561000	Weak transcription	Stomach Mucosa	stomach
11	chr11:47546800-47559000	Strong transcription	Fetal Intestine Small	intestine
12	chr11:47546800-47560200	Weak transcription	Primary hematopoietic stem cells	blood
13	chr11:47547200-47559600	Weak transcription	HUVEC	blood vessel
14	chr11:47547400-47558000	Weak transcription	Small Intestine	intestine
15	chr11:47547400-47560400	Weak transcription	HUES48 Cell Line	embryonic stem cell
16	chr11:47547400-47560800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr11:47547800-47562000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:47548200-47560400	Weak transcription	HUES6 Cell Line	embryonic stem cell
19	chr11:47549000-47559400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:47550400-47559200	Weak transcription	NHEK	skin
21	chr11:47550600-47561000	Weak transcription	Placenta	Placenta
22	chr11:47550800-47558000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr11:47551000-47563200	Enhancers	Fetal Brain Male	brain
24	chr11:47551200-47559000	Weak transcription	Psoas Muscle	Psoas
25	chr11:47552200-47560400	Weak transcription	HMEC	breast
26	chr11:47552600-47560800	Weak transcription	Pancreas	Pancrea
27	chr11:47553000-47573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:47554200-47561400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
29	chr11:47554400-47559400	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr11:47554400-47560200	Weak transcription	Brain Angular Gyrus	brain
31	chr11:47554400-47560400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:47554400-47561200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr11:47554400-47561600	Weak transcription	Fetal Kidney	kidney
34	chr11:47554400-47572400	Weak transcription	Aorta	Aorta
35	chr11:47554600-47558000	Weak transcription	Right Atrium	heart
36	chr11:47554600-47558000	Weak transcription	Dnd41	blood
37	chr11:47554600-47559400	Weak transcription	Brain Germinal Matrix	brain
38	chr11:47554600-47559400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:47554600-47560400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr11:47554600-47560400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr11:47554600-47560400	Weak transcription	NHDF-Ad	bronchial
42	chr11:47554600-47561200	Weak transcription	HepG2	liver
43	chr11:47554800-47558000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr11:47554800-47559600	Strong transcription	Hela-S3	cervix
45	chr11:47554800-47571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
46	chr11:47554800-47572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr11:47555000-47559400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:47555000-47560200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr11:47555000-47560400	Weak transcription	Gastric	stomach
50	chr11:47555000-47560800	Weak transcription	H1 Cell Line	embryonic stem cell

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