Variant report

Variant	rs17128050
Chromosome Location	chr14:55343879-55343880
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: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10133449	0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10134163	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10145097	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10146658	0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10498471	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap]
rs12147422	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2183080	0.88[CEU][hapmap]
rs28477407	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28542181	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28757745	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34429973	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3783637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs3783638	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap]
rs4363780	0.85[EUR][1000 genomes]
rs4402455	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57575708	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61702394	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7141319	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7141433	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73280512	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7492600	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8004018	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs8010282	1.00[CEU][hapmap]
rs8010689	0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs17128050	GCH1	cis	cerebellum	SCAN
rs17128050	WDHD1	cis	cerebellum	SCAN
rs17128050	L2HGDH	cis	parietal	SCAN
rs17128050	KTN1	cis	cerebellum	SCAN
rs17128050	GCH1	cis	parietal	SCAN

Chromatin state (count:36 , 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	chr14:55331800-55344800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr14:55331800-55347600	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr14:55334000-55346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr14:55337200-55345000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr14:55337400-55346000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr14:55337400-55346200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr14:55337400-55347800	Weak transcription	HSMMtube	muscle
10	chr14:55337600-55346400	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr14:55337600-55348600	Weak transcription	Hela-S3	cervix
12	chr14:55337800-55345600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr14:55338000-55346000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr14:55338200-55344000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr14:55338400-55344600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr14:55341000-55345800	Weak transcription	Liver	Liver
17	chr14:55343200-55344000	Enhancers	Fetal Intestine Small	intestine
18	chr14:55343200-55344400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr14:55343400-55344000	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr14:55343400-55344800	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr14:55343400-55344800	Enhancers	Primary hematopoietic stem cells	blood
22	chr14:55343600-55344200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr14:55343600-55344200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
24	chr14:55343600-55344200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr14:55343600-55344200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
26	chr14:55343600-55345000	Enhancers	Duodenum Mucosa	Duodenum
27	chr14:55343600-55345000	Enhancers	HepG2	liver
28	chr14:55343800-55344000	Enhancers	Primary T cells from cord blood	blood
29	chr14:55343800-55344000	Enhancers	HUVEC	blood vessel
30	chr14:55343800-55344200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr14:55343800-55344200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
32	chr14:55343800-55344200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr14:55343800-55344200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr14:55343800-55345200	Enhancers	iPS-15b Cell Line	embryonic stem cell
35	chr14:55343800-55347800	Weak transcription	Rectal Mucosa Donor 31	rectum
36	chr14:55343800-55348200	Weak transcription	Fetal Intestine Large	intestine

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