Variant report

Variant	rs28477407
Chromosome Location	chr14:55344901-55344902
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55343213..55346860-chr14:55368496..55370471,3	MCF-7	breast:
2	chr14:55343813..55346930-chr14:55349782..55354238,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000131979	Chromatin interaction
ENSG00000258872	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10133449	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10134163	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10139282	0.80[ASN][1000 genomes]
rs10145097	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10146658	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10498471	0.80[ASN][1000 genomes]
rs10873086	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs11158027	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12147422	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17128050	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28542181	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28757745	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34429973	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3783637	0.80[ASN][1000 genomes]
rs3783638	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs3825611	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4363780	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4402455	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57575708	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61702394	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7141319	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7141433	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73280512	0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7492600	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8004018	0.80[ASN][1000 genomes]
rs8004445	0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs8010461	0.80[ASN][1000 genomes]
rs8010689	0.82[EUR][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
rs28477407	GCH1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55329400-55347800	Weak transcription	Primary B cells from cord blood	blood
2	chr14:55330800-55347800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr14:55331800-55347600	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr14:55334000-55346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr14:55337200-55345000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr14:55337400-55346000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr14:55337400-55346200	Weak transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:55337400-55347800	Weak transcription	HSMMtube	muscle
9	chr14:55337600-55346400	Weak transcription	Primary T helper cells fromperipheralblood	blood
10	chr14:55337600-55348600	Weak transcription	Hela-S3	cervix
11	chr14:55337800-55345600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr14:55338000-55346000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr14:55341000-55345800	Weak transcription	Liver	Liver
14	chr14:55343600-55345000	Enhancers	Duodenum Mucosa	Duodenum
15	chr14:55343600-55345000	Enhancers	HepG2	liver
16	chr14:55343800-55345200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr14:55343800-55347800	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr14:55343800-55348200	Weak transcription	Fetal Intestine Large	intestine
19	chr14:55344000-55345000	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr14:55344000-55345200	Enhancers	iPS-18 Cell Line	embryonic stem cell
21	chr14:55344000-55345400	Enhancers	GM12878-XiMat	blood
22	chr14:55344000-55345600	Weak transcription	Fetal Intestine Small	intestine
23	chr14:55344000-55346800	Weak transcription	Primary T cells from cord blood	blood
24	chr14:55344000-55347800	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr14:55344200-55345000	Enhancers	HUVEC	blood vessel
26	chr14:55344200-55345600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:55344200-55345800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr14:55344200-55346200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr14:55344200-55346200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
30	chr14:55344200-55346200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr14:55344200-55346200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr14:55344200-55347600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr14:55344400-55347800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr14:55344600-55345000	Enhancers	HUES64 Cell Line	embryonic stem cell
35	chr14:55344600-55345200	Enhancers	HUES48 Cell Line	embryonic stem cell
36	chr14:55344800-55345000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr14:55344800-55345000	Enhancers	iPS-20b Cell Line	embryonic stem cell
38	chr14:55344800-55345200	Enhancers	H1 Cell Line	embryonic stem cell
39	chr14:55344800-55345400	Enhancers	H9 Cell Line	embryonic stem cell
40	chr14:55344800-55345400	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr14:55344800-55345400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr14:55344800-55345800	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr14:55344800-55346400	Weak transcription	Primary hematopoietic stem cells	blood

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