Variant report

Variant	rs10838726
Chromosome Location	chr11:47568344-47568345
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47556325..47561893-chr11:47562676..47568878,7	K562	blood:
2	chr11:47565515..47568693-chr11:47572907..47576173,5	K562	blood:
3	chr11:47557985..47562133-chr11:47565496..47569267,5	K562	blood:
4	chr11:47564735..47568693-chr11:47572355..47576179,6	K562	blood:
5	chr11:47559176..47561794-chr11:47565770..47569453,3	MCF-7	breast:
6	chr11:47543279..47546104-chr11:47567027..47568704,2	K562	blood:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1017730	0.81[CHB][hapmap]
rs1056387	0.89[JPT][hapmap]
rs10742814	0.95[JPT][hapmap]
rs10742817	0.84[JPT][hapmap]
rs10769264	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10769282	0.81[ASN][1000 genomes]
rs10838702	0.94[CHB][hapmap]
rs10838709	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs10838725	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10838731	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10838732	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10838740	0.89[JPT][hapmap]
rs10838746	0.88[JPT][hapmap]
rs11039225	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs11039244	0.88[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs11039266	0.91[CEU][hapmap]
rs11039280	1.00[JPT][hapmap]
rs11039284	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs11039290	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039297	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11039329	0.89[JPT][hapmap]
rs11039332	0.91[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes]
rs11039345	0.89[JPT][hapmap]
rs12225051	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12226590	0.85[ASN][1000 genomes]
rs12286721	0.89[JPT][hapmap]
rs12287076	0.85[EUR][1000 genomes]
rs12292911	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12361415	0.87[CEU][hapmap]
rs12365079	0.80[AMR][1000 genomes]
rs12577643	0.88[CEU][hapmap]
rs12785949	0.88[JPT][hapmap]
rs1377416	0.94[CHB][hapmap]
rs1534576	0.87[CHB][hapmap]
rs1563821	0.84[JPT][hapmap]
rs2203712	0.95[JPT][hapmap]
rs2242081	0.95[JPT][hapmap]
rs2280231	0.91[CEU][hapmap];0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2290851	0.89[JPT][hapmap]
rs2293576	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs3740699	0.84[JPT][hapmap]
rs3758655	0.89[JPT][hapmap]
rs4539273	0.89[JPT][hapmap]
rs4752860	0.89[JPT][hapmap]
rs4752865	0.89[JPT][hapmap]
rs6485758	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes]
rs6485763	0.95[JPT][hapmap]
rs6485773	0.89[JPT][hapmap]
rs7103648	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs7118178	0.86[CEU][hapmap];0.83[CHB][hapmap]
rs7120548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7126378	0.83[ASN][1000 genomes]
rs7129797	0.89[JPT][hapmap]
rs71475921	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7933019	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes]
rs7936948	0.89[JPT][hapmap]
rs7939420	0.89[JPT][hapmap]
rs7950696	0.95[JPT][hapmap]
rs874896	0.88[CHB][hapmap]
rs896817	0.94[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv314	chr11:47561564-47606256	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
5	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10838726	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838726	C1QTNF4	cis	multi-tissue	Pritchard
rs10838726	FNBP4	cis	lesional skin	skin_eQTL

Chromatin state (count:113 , 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	chr11:47546400-47573400	Weak transcription	Colonic Mucosa	Colon
3	chr11:47546400-47573600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47553000-47573200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr11:47554400-47572400	Weak transcription	Aorta	Aorta
6	chr11:47554800-47571600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:47554800-47572400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:47558400-47572600	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr11:47559000-47571800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr11:47559600-47572600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr11:47561600-47573200	Weak transcription	Placenta	Placenta
12	chr11:47562000-47570600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr11:47562000-47571800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr11:47562000-47572600	Weak transcription	Brain Substantia Nigra	brain
15	chr11:47562200-47569000	Weak transcription	Pancreas	Pancrea
16	chr11:47562200-47571200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr11:47562200-47572000	Weak transcription	Rectal Smooth Muscle	rectum
18	chr11:47562200-47572600	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr11:47562200-47572800	Weak transcription	Fetal Kidney	kidney
20	chr11:47562400-47569200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr11:47562400-47572200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:47562600-47569200	Weak transcription	A549	lung
23	chr11:47562600-47569400	Weak transcription	Primary B cells from cord blood	blood
24	chr11:47562600-47570600	Weak transcription	Fetal Brain Female	brain
25	chr11:47562600-47570800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:47562600-47571600	Weak transcription	Right Atrium	heart
27	chr11:47562600-47571800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr11:47562600-47572400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:47562600-47572400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr11:47562600-47572400	Weak transcription	Right Ventricle	heart
31	chr11:47562600-47573200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:47562800-47569200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr11:47562800-47569200	Weak transcription	Osteobl	bone
34	chr11:47562800-47569400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr11:47562800-47570600	Weak transcription	Dnd41	blood
36	chr11:47562800-47571200	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:47562800-47572200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr11:47562800-47572200	Weak transcription	NH-A	brain
39	chr11:47562800-47572200	Weak transcription	NHLF	lung
40	chr11:47562800-47572400	Weak transcription	Stomach Mucosa	stomach
41	chr11:47562800-47572400	Weak transcription	NHDF-Ad	bronchial
42	chr11:47563000-47568600	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr11:47563000-47570800	Weak transcription	Primary hematopoietic stem cells	blood
44	chr11:47563000-47570800	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:47563000-47570800	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:47563000-47571000	Weak transcription	HUVEC	blood vessel
47	chr11:47563000-47572000	Weak transcription	HMEC	breast
48	chr11:47563000-47572000	Weak transcription	HSMM	muscle
49	chr11:47563600-47571200	Weak transcription	K562	blood
50	chr11:47563800-47571600	Weak transcription	Fetal Brain Male	brain

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