Variant report

Variant	rs11039354
Chromosome Location	chr11:47735154-47735155
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47734421..47738084-chr11:47868728..47871724,4	K562	blood:
2	chr11:47733134..47735663-chr11:47755536..47757163,2	MCF-7	breast:
3	chr11:47733919..47739426-chr11:47787626..47790588,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000109920	Chromatin interaction
ENSG00000030066	Chromatin interaction

Extended variants
information (count: 100 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1056387	0.84[EUR][1000 genomes]
rs10742817	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10742820	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10769285	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10769299	0.80[EUR][1000 genomes]
rs10838739	0.81[EUR][1000 genomes]
rs10838740	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838741	0.84[EUR][1000 genomes]
rs10838745	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10838746	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10838751	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10838758	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838759	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838760	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10838763	0.87[EUR][1000 genomes]
rs10838766	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs10838768	0.83[EUR][1000 genomes]
rs10838769	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs10838771	0.85[EUR][1000 genomes]
rs10838773	0.81[EUR][1000 genomes]
rs10838775	0.80[EUR][1000 genomes]
rs10838782	0.81[EUR][1000 genomes]
rs11039329	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039336	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11039337	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039345	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039373	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039376	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039377	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039379	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11039392	0.87[EUR][1000 genomes]
rs11039401	0.83[EUR][1000 genomes]
rs11039402	0.83[EUR][1000 genomes]
rs11039414	0.85[EUR][1000 genomes]
rs12226431	0.85[EUR][1000 genomes]
rs12286721	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12360643	0.89[EUR][1000 genomes]
rs12362318	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12421563	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12785949	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563820	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs1563821	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2125838	0.83[EUR][1000 genomes]
rs2290851	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs28617307	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2869534	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2869541	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2904127	0.83[EUR][1000 genomes]
rs3758655	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3886262	0.83[EUR][1000 genomes]
rs4539273	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4543938	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4752792	0.85[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4752796	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4752798	0.81[EUR][1000 genomes]
rs4752858	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752860	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752865	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs60833259	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs61895760	0.87[EUR][1000 genomes]
rs6485773	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6485775	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6485778	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6485786	0.83[EUR][1000 genomes]
rs7101597	0.87[EUR][1000 genomes]
rs7102205	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7105791	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7107792	0.81[EUR][1000 genomes]
rs7108479	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7111509	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7111576	0.86[EUR][1000 genomes]
rs7111606	0.87[EUR][1000 genomes]
rs7112248	0.80[EUR][1000 genomes]
rs7114813	0.85[EUR][1000 genomes]
rs7115228	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7116320	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7116346	0.80[EUR][1000 genomes]
rs7116970	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7118747	0.82[EUR][1000 genomes]
rs7122182	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7122217	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7123952	0.80[EUR][1000 genomes]
rs7124396	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7129237	0.86[EUR][1000 genomes]
rs754434	0.83[EUR][1000 genomes]
rs7925211	0.85[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs7929014	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7932703	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7933184	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7935344	0.81[EUR][1000 genomes]
rs7935521	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7935528	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7936948	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7939420	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7943213	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7948468	0.81[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs7950674	0.80[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	nsv469858	chr11:47647515-47837172	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
3	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11039354	FNBP4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47705600-47735600	Weak transcription	Primary B cells from cord blood	blood
2	chr11:47712000-47736000	Weak transcription	Fetal Intestine Small	intestine
3	chr11:47722400-47735800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr11:47729200-47736000	Weak transcription	Hela-S3	cervix
5	chr11:47732200-47735800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr11:47732200-47736000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:47732400-47735800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr11:47732400-47736000	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr11:47732400-47736000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr11:47732400-47736000	Weak transcription	Osteobl	bone
11	chr11:47732400-47737600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:47732600-47735600	Weak transcription	Brain Anterior Caudate	brain
13	chr11:47732800-47735600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr11:47733000-47735800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr11:47733000-47736800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr11:47733200-47735400	Weak transcription	HepG2	liver
17	chr11:47733200-47735800	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr11:47733200-47736000	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr11:47733200-47736200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr11:47733400-47736000	Weak transcription	Pancreas	Pancrea
21	chr11:47733600-47736200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr11:47733800-47735400	Weak transcription	Liver	Liver
23	chr11:47734200-47736000	Weak transcription	HSMM	muscle
24	chr11:47734400-47735800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr11:47734400-47735800	Weak transcription	Fetal Lung	lung
26	chr11:47734800-47735800	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr11:47735000-47735800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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