Variant report

Variant	rs10873086
Chromosome Location	chr14:55349258-55349259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA2	chr14:55348885-55349852	SH-SY5Y	brain:	n/a	chr14:55349576-55349589 chr14:55349578-55349588 chr14:55349573-55349594 chr14:55349578-55349587 chr14:55349575-55349591 chr14:55349580-55349587
2	RFX5	chr14:55348044-55349924	SK-N-SH	brain:	n/a	chr14:55349620-55349629 chr14:55349597-55349605
3	YY1	chr14:55349249-55349697	SK-N-SH_RA	brain:	n/a	n/a
4	GATA3	chr14:55348933-55349784	SH-SY5Y	brain:	n/a	chr14:55349576-55349589 chr14:55349578-55349588 chr14:55349573-55349594 chr14:55349578-55349587 chr14:55349575-55349591 chr14:55349580-55349587
5	EP300	chr14:55349217-55349737	SK-N-SH_RA	brain:	n/a	n/a
6	GATA3	chr14:55348797-55349833	SK-N-SH	brain:	n/a	chr14:55349576-55349589 chr14:55349578-55349588 chr14:55349573-55349594 chr14:55349578-55349587 chr14:55349575-55349591 chr14:55349580-55349587
7	GATA1	chr14:55348381-55349698	PBDE	blood:	n/a	chr14:55349576-55349589 chr14:55349578-55349588 chr14:55349573-55349594 chr14:55349578-55349587 chr14:55349575-55349591 chr14:55349580-55349587
8	GATA3	chr14:55349006-55349825	SK-N-SH	brain:	n/a	chr14:55349576-55349589 chr14:55349578-55349588 chr14:55349573-55349594 chr14:55349578-55349587 chr14:55349575-55349591 chr14:55349580-55349587
9	POLR2A	chr14:55349205-55349652	SK-N-SH	brain:	n/a	n/a
10	EP300	chr14:55347820-55350131	SK-N-SH	brain:	n/a	chr14:55348166-55348180 chr14:55348796-55348810 chr14:55348744-55348752
11	IRF1	chr14:55348012-55349360	K562	blood:	n/a	chr14:55348193-55348206 chr14:55348801-55348815 chr14:55348190-55348204 chr14:55348801-55348811 chr14:55348194-55348208 chr14:55348193-55348206 chr14:55348797-55348811 chr14:55348188-55348205 chr14:55348193-55348206 chr14:55349323-55349339 chr14:55348172-55348188 chr14:55348194-55348204 chr14:55348801-55348812 chr14:55348799-55348812 chr14:55348192-55348203 chr14:55348802-55348813 chr14:55348193-55348207 chr14:55348799-55348812 chr14:55348799-55348812 chr14:55348464-55348478 chr14:55348193-55348204
12	MXI1	chr14:55347817-55349899	SK-N-SH	brain:	n/a	n/a
13	EP300	chr14:55349085-55349698	SK-N-SH_RA	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:55349065..55350760-chr14:55354451..55355964,2	K562	blood:
2	chr14:55344081..55346333-chr14:55348656..55350611,2	K562	blood:
3	chr14:55348331..55350043-chr14:55361093..55363707,2	K562	blood:

Variant related genes	Relation type
MIR4308	TF binding region
ENSG00000265432	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10133449	0.82[AFR][1000 genomes]
rs10139282	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498471	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147422	0.82[AFR][1000 genomes]
rs2183080	0.83[EUR][1000 genomes]
rs28477407	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs28542181	0.81[AFR][1000 genomes]
rs28757745	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3783637	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783638	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825611	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702394	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs66989494	0.83[EUR][1000 genomes]
rs8003903	0.92[EUR][1000 genomes]
rs8004018	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8004445	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010461	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10873086	GCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55345400-55354800	Weak transcription	HUES6 Cell Line	embryonic stem cell
2	chr14:55345400-55368200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr14:55347600-55349400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr14:55347600-55349400	Flanking Active TSS	Dnd41	blood
5	chr14:55347800-55349600	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr14:55348000-55349600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr14:55348000-55349600	Enhancers	HepG2	liver
8	chr14:55348000-55349800	Flanking Active TSS	Fetal Lung	lung
9	chr14:55348000-55355000	Weak transcription	Small Intestine	intestine
10	chr14:55348400-55349400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr14:55348400-55356000	Weak transcription	Lung	lung
12	chr14:55348400-55368200	Weak transcription	Gastric	stomach
13	chr14:55348600-55349600	Enhancers	Sigmoid Colon	Sigmoid Colon
14	chr14:55348600-55349600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr14:55348600-55354800	Weak transcription	Esophagus	oesophagus
16	chr14:55348800-55349400	Enhancers	Fetal Kidney	kidney
17	chr14:55348800-55349400	Enhancers	Stomach Mucosa	stomach
18	chr14:55348800-55349400	Flanking Active TSS	GM12878-XiMat	blood
19	chr14:55349000-55349400	Enhancers	Primary B cells from cord blood	blood
20	chr14:55349000-55349400	Enhancers	Primary B cells from peripheral blood	blood
21	chr14:55349000-55349400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr14:55349000-55349400	Enhancers	Fetal Intestine Small	intestine
23	chr14:55349000-55349400	Active TSS	Skeletal Muscle Female	skeletal muscle
24	chr14:55349000-55349600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr14:55349000-55349600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
26	chr14:55349000-55349600	Enhancers	Adipose Nuclei	Adipose
27	chr14:55349000-55349600	Enhancers	Brain Inferior Temporal Lobe	brain
28	chr14:55349000-55349600	Enhancers	Colonic Mucosa	Colon
29	chr14:55349000-55349800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr14:55349000-55349800	Enhancers	Primary T cells from cord blood	blood
31	chr14:55349000-55349800	Enhancers	Liver	Liver
32	chr14:55349000-55349800	Enhancers	Placenta	Placenta
33	chr14:55349000-55350000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr14:55349000-55350000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr14:55349000-55350600	Enhancers	Primary T cells fromperipheralblood	blood
36	chr14:55349000-55351200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr14:55349000-55352000	Weak transcription	Aorta	Aorta
38	chr14:55349000-55352400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr14:55349000-55353000	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr14:55349000-55353200	Weak transcription	Fetal Muscle Leg	muscle
41	chr14:55349000-55353400	Weak transcription	Brain Anterior Caudate	brain
42	chr14:55349000-55355000	Weak transcription	K562	blood
43	chr14:55349000-55366400	Weak transcription	Hela-S3	cervix
44	chr14:55349200-55349400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr14:55349200-55349400	Enhancers	Rectal Mucosa Donor 31	rectum
46	chr14:55349200-55349600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr14:55349200-55349600	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr14:55349200-55349600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
49	chr14:55349200-55349600	Enhancers	Duodenum Smooth Muscle	Duodenum
50	chr14:55349200-55349600	Enhancers	HSMMtube	muscle

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