Variant report

Variant	rs11879271
Chromosome Location	chr19:40447021-40447022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:40439263..40441192-chr19:40446766..40448427,2	K562	blood:
2	chr19:40445775..40448041-chr19:40449337..40452328,2	MCF-7	breast:
3	chr19:40446423..40448525-chr19:40595370..40597652,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000269749	Chromatin interaction
ENSG00000187534	Chromatin interaction
ENSG00000090920	Chromatin interaction
ENSG00000269296	Chromatin interaction
ENSG00000197782	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11878670	0.82[ASN][1000 genomes]
rs11880843	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs11883342	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes]
rs12052060	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12052169	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs3760921	1.00[YRI][hapmap];0.98[AFR][1000 genomes]
rs55673424	0.82[ASN][1000 genomes]
rs55718963	0.82[ASN][1000 genomes]
rs55838062	0.81[AFR][1000 genomes]
rs55873814	0.82[ASN][1000 genomes]
rs56040936	0.96[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56108413	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7250934	0.82[ASN][1000 genomes]
rs73040535	0.82[ASN][1000 genomes]
rs73040537	0.82[ASN][1000 genomes]
rs73040556	0.81[AFR][1000 genomes]
rs73040573	0.84[AFR][1000 genomes]
rs73052616	0.92[AFR][1000 genomes]
rs73052630	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73052632	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
6	nsv978815	chr19:40443651-40449610	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11879271	FCGBP	cis	multi-tissue	Pritchard

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40441200-40449000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr19:40441800-40447200	Weak transcription	Esophagus	oesophagus
3	chr19:40442000-40450400	Weak transcription	Brain Substantia Nigra	brain
4	chr19:40442400-40449000	Weak transcription	Pancreas	Pancrea
5	chr19:40442400-40450400	Weak transcription	Lung	lung
6	chr19:40445400-40447400	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
7	chr19:40445600-40447600	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr19:40446000-40447200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr19:40446200-40447200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr19:40446200-40447600	ZNF genes & repeats	A549	lung
11	chr19:40446200-40447800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
12	chr19:40446600-40447800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr19:40446600-40449200	Flanking Active TSS	Dnd41	blood
14	chr19:40446800-40447200	Enhancers	Primary B cells from peripheral blood	blood
15	chr19:40446800-40447200	Enhancers	Duodenum Mucosa	Duodenum
16	chr19:40446800-40447800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
17	chr19:40446800-40447800	Flanking Active TSS	GM12878-XiMat	blood
18	chr19:40446800-40448400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:40446800-40448400	Flanking Active TSS	Primary T cells from cord blood	blood
20	chr19:40446800-40448400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
21	chr19:40446800-40448400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
22	chr19:40446800-40448800	Enhancers	Primary hematopoietic stem cells	blood
23	chr19:40446800-40451600	Enhancers	Sigmoid Colon	Sigmoid Colon
24	chr19:40446800-40453000	Enhancers	Fetal Intestine Large	intestine
25	chr19:40446800-40453000	Enhancers	Stomach Mucosa	stomach
26	chr19:40447000-40447200	Enhancers	Fetal Muscle Trunk	muscle
27	chr19:40447000-40447400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr19:40447000-40447400	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:40447000-40447400	Enhancers	Placenta	Placenta
30	chr19:40447000-40447400	Active TSS	Rectal Smooth Muscle	rectum
31	chr19:40447000-40447600	ZNF genes & repeats	Brain Hippocampus Middle	brain
32	chr19:40447000-40447600	Enhancers	Colonic Mucosa	Colon
33	chr19:40447000-40447600	Enhancers	Small Intestine	intestine
34	chr19:40447000-40447800	Enhancers	H1 Cell Line	embryonic stem cell
35	chr19:40447000-40447800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr19:40447000-40447800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
37	chr19:40447000-40447800	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
38	chr19:40447000-40447800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
39	chr19:40447000-40447800	Enhancers	Spleen	Spleen
40	chr19:40447000-40448000	Enhancers	Gastric	stomach
41	chr19:40447000-40448200	Enhancers	Brain Germinal Matrix	brain
42	chr19:40447000-40448400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
43	chr19:40447000-40448400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
44	chr19:40447000-40448400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
45	chr19:40447000-40448400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
46	chr19:40447000-40448600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr19:40447000-40448600	Flanking Active TSS	Primary B cells from cord blood	blood
48	chr19:40447000-40448600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr19:40447000-40448600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr19:40447000-40449200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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