Variant report

Variant	rs2278890
Chromosome Location	chr11:47399602-47399603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47397121..47400538-chr11:47420513..47424481,4	K562	blood:
2	chr11:47398113..47400151-chr11:47419730..47422644,3	K562	blood:
3	chr11:47278014..47279566-chr11:47397375..47399995,2	K562	blood:
4	chr11:47395359..47404298-chr11:47408556..47417905,22	K562	blood:
5	chr11:47397140..47399846-chr11:47404698..47406803,2	MCF-7	breast:
6	chr11:47394067..47402014-chr11:47426765..47432976,19	K562	blood:
7	chr11:47289554..47292260-chr11:47397624..47400665,3	K562	blood:
8	chr11:47399004..47400770-chr11:47446343..47448819,3	K562	blood:
9	chr11:47391440..47404809-chr11:47427075..47436409,23	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264583	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000165916	Chromatin interaction
ENSG00000165915	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000255197	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10437655	0.90[EUR][1000 genomes]
rs10742802	0.82[EUR][1000 genomes]
rs10769263	0.86[EUR][1000 genomes]
rs10769264	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs10838702	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs10838703	0.84[CEU][hapmap];0.86[CHB][hapmap]
rs10838705	0.83[EUR][1000 genomes]
rs10838709	0.92[CEU][hapmap]
rs11039221	0.83[EUR][1000 genomes]
rs11039225	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs11039266	0.92[CHB][hapmap]
rs11602333	1.00[YRI][hapmap]
rs11605061	1.00[YRI][hapmap]
rs11606287	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11607518	1.00[YRI][hapmap]
rs12292911	0.92[CEU][hapmap]
rs1377416	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs1534576	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs2293579	0.82[EUR][1000 genomes]
rs2697923	0.81[CEU][hapmap]
rs34937994	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35032070	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758675	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3824869	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7103648	0.92[CEU][hapmap]
rs7103835	0.81[CEU][hapmap];0.87[CHB][hapmap]
rs71475909	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7947450	0.83[EUR][1000 genomes]
rs874896	0.92[CEU][hapmap];0.83[EUR][1000 genomes]
rs896817	0.92[CEU][hapmap];0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
3	esv3330173	chr11:47289256-47450681	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
4	esv3416377	chr11:47289276-47450651	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
5	nsv832141	chr11:47333180-47520993	Flanking Active TSS Genic enhancers Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
6	nsv825871	chr11:47376020-47457537	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv554210	chr11:47380593-47449544	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2278890	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs2278890	C1QTNF4	cis	multi-tissue	Pritchard

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47395200-47410000	Weak transcription	Gastric	stomach
2	chr11:47396400-47400000	Active TSS	Brain Hippocampus Middle	brain
3	chr11:47396600-47400400	Active TSS	Rectal Mucosa Donor 29	rectum
4	chr11:47396800-47400400	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr11:47397000-47400400	Active TSS	Placenta	Placenta
6	chr11:47397200-47400000	Active TSS	Stomach Smooth Muscle	stomach
7	chr11:47397200-47400800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr11:47397400-47400400	Active TSS	Colonic Mucosa	Colon
9	chr11:47397400-47401200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr11:47397600-47399800	Active TSS	Skeletal Muscle Female	skeletal muscle
11	chr11:47397600-47400000	Active TSS	Adipose Nuclei	Adipose
12	chr11:47397600-47400000	Active TSS	Liver	Liver
13	chr11:47397600-47400000	Active TSS	Brain Anterior Caudate	brain
14	chr11:47397600-47400000	Active TSS	Brain Cingulate Gyrus	brain
15	chr11:47397600-47400200	Active TSS	Duodenum Mucosa	Duodenum
16	chr11:47397800-47399800	Active TSS	Brain Substantia Nigra	brain
17	chr11:47397800-47399800	Active TSS	Pancreas	Pancrea
18	chr11:47397800-47399800	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr11:47397800-47400000	Active TSS	Primary monocytes fromperipheralblood	blood
20	chr11:47397800-47400000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr11:47397800-47400000	Active TSS	Fetal Intestine Large	intestine
22	chr11:47397800-47400000	Active TSS	Fetal Intestine Small	intestine
23	chr11:47397800-47400000	Active TSS	Rectal Smooth Muscle	rectum
24	chr11:47397800-47400600	Flanking Active TSS	K562	blood
25	chr11:47397800-47400800	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr11:47398000-47399800	Active TSS	Left Ventricle	heart
27	chr11:47398000-47400000	Active TSS	Lung	lung
28	chr11:47398200-47400000	Active TSS	Spleen	Spleen
29	chr11:47398200-47400200	Active TSS	GM12878-XiMat	blood
30	chr11:47398200-47400400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:47398200-47400600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr11:47398400-47399800	Active TSS	Fetal Stomach	stomach
33	chr11:47398400-47399800	Active TSS	Right Atrium	heart
34	chr11:47398400-47400000	Active TSS	Primary T helper cells fromperipheralblood	blood
35	chr11:47398400-47400000	Flanking Active TSS	Fetal Muscle Trunk	muscle
36	chr11:47398400-47400200	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr11:47398600-47400200	Enhancers	Fetal Heart	heart
38	chr11:47398600-47400800	Enhancers	ES-I3 Cell Line	embryonic stem cell
39	chr11:47398800-47399800	Active TSS	Esophagus	oesophagus
40	chr11:47398800-47400000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
41	chr11:47398800-47400000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr11:47398800-47400000	Active TSS	Thymus	Thymus
43	chr11:47398800-47400200	Weak transcription	HUES6 Cell Line	embryonic stem cell
44	chr11:47398800-47400200	Active TSS	Primary B cells from peripheral blood	blood
45	chr11:47399000-47399800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr11:47399000-47399800	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr11:47399000-47400200	Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr11:47399200-47399800	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr11:47399200-47399800	Active TSS	Brain Angular Gyrus	brain
50	chr11:47399200-47399800	Enhancers	Right Ventricle	heart

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