Variant report

Variant	rs8004018
Chromosome Location	chr14:55350696-55350697
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55349065..55350760-chr14:55354451..55355964,2	K562	blood:
2	chr14:55343813..55346930-chr14:55349782..55354238,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000265432	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10139282	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10498471	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873086	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11158027	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12147422	1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[JPT][hapmap];0.93[YRI][hapmap]
rs17128050	1.00[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs2183080	0.85[CEU][hapmap];0.83[EUR][1000 genomes]
rs28477407	0.80[ASN][1000 genomes]
rs28757745	0.80[ASN][1000 genomes]
rs3783637	1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783638	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.93[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3825611	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61702394	0.80[ASN][1000 genomes]
rs66989494	0.83[EUR][1000 genomes]
rs7492600	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs8003903	0.92[EUR][1000 genomes]
rs8004445	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8010282	1.00[CEU][hapmap];0.92[YRI][hapmap]
rs8010461	0.85[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs8004018	KTN1	cis	cerebellum	SCAN
rs8004018	GCH1	Cis_1M	lymphoblastoid	RTeQTL
rs8004018	WDHD1	cis	cerebellum	SCAN
rs8004018	GCH1	cis	cerebellum	SCAN
rs8004018	L2HGDH	cis	parietal	SCAN
rs8004018	GCH1	cis	parietal	SCAN

Chromatin state (count:49 , 50 per page) page: 1

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	chr14:55348000-55355000	Weak transcription	Small Intestine	intestine
4	chr14:55348400-55356000	Weak transcription	Lung	lung
5	chr14:55348400-55368200	Weak transcription	Gastric	stomach
6	chr14:55348600-55354800	Weak transcription	Esophagus	oesophagus
7	chr14:55349000-55351200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr14:55349000-55352000	Weak transcription	Aorta	Aorta
9	chr14:55349000-55352400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr14:55349000-55353000	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr14:55349000-55353200	Weak transcription	Fetal Muscle Leg	muscle
12	chr14:55349000-55353400	Weak transcription	Brain Anterior Caudate	brain
13	chr14:55349000-55355000	Weak transcription	K562	blood
14	chr14:55349000-55366400	Weak transcription	Hela-S3	cervix
15	chr14:55349200-55351000	Enhancers	NHEK	skin
16	chr14:55349200-55351400	Weak transcription	Primary hematopoietic stem cells	blood
17	chr14:55349200-55354800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr14:55349200-55357800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:55349200-55358400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr14:55349200-55367400	Weak transcription	Fetal Intestine Large	intestine
21	chr14:55349200-55367400	Weak transcription	Thymus	Thymus
22	chr14:55349400-55351200	Enhancers	Primary T helper cells PMA-I stimulated	--
23	chr14:55349400-55352800	Weak transcription	Primary B cells from peripheral blood	blood
24	chr14:55349400-55353400	Weak transcription	GM12878-XiMat	blood
25	chr14:55349400-55355000	Weak transcription	Fetal Kidney	kidney
26	chr14:55349400-55356400	Weak transcription	Fetal Intestine Small	intestine
27	chr14:55349400-55367800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr14:55349600-55351600	Weak transcription	HepG2	liver
29	chr14:55349600-55353800	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr14:55349600-55355800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr14:55349600-55355800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr14:55349600-55355800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr14:55349600-55367200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr14:55349600-55368000	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr14:55349800-55351600	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr14:55349800-55351600	Weak transcription	Liver	Liver
37	chr14:55349800-55353400	Weak transcription	Primary T cells from cord blood	blood
38	chr14:55349800-55353400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr14:55349800-55355000	Weak transcription	Fetal Lung	lung
40	chr14:55350000-55366400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr14:55350200-55351200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr14:55350200-55351400	Enhancers	Primary T helper cells fromperipheralblood	blood
43	chr14:55350400-55350800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr14:55350400-55350800	Enhancers	HMEC	breast
45	chr14:55350400-55351000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:55350400-55351000	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr14:55350600-55351600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr14:55350600-55351600	Weak transcription	Monocytes-CD14+_RO01746	blood
49	chr14:55350600-55352000	Weak transcription	Primary T cells fromperipheralblood	blood

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