Variant report

Variant	rs2183081
Chromosome Location	chr14:55336751-55336752
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	chr14:55329931..55332245-chr14:55336217..55337731,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10131232	0.85[ASW][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];0.95[YRI][hapmap]
rs10133650	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10133662	0.95[YRI][hapmap]
rs10136545	0.83[ASN][1000 genomes]
rs1107960	0.91[CEU][hapmap]
rs11158024	0.86[YRI][hapmap]
rs11158026	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11626298	0.81[AFR][1000 genomes]
rs12323905	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17128120	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs2183082	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2183084	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28417208	0.83[ASN][1000 genomes]
rs2878172	0.88[YRI][hapmap]
rs3783640	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3783642	0.89[GIH][hapmap];0.82[LWK][hapmap];0.91[YRI][hapmap]
rs4462519	0.81[AFR][1000 genomes]
rs7144602	0.87[MKK][hapmap];0.95[YRI][hapmap]
rs7146285	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs7147286	0.88[CEU][hapmap];0.91[YRI][hapmap]
rs7155501	0.83[ASN][1000 genomes]
rs8007201	0.85[ASW][hapmap];0.88[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap]
rs8012152	0.88[CEU][hapmap];0.85[TSI][hapmap]
rs8018355	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8023187	0.86[YRI][hapmap]
rs9989242	0.83[AMR][1000 genomes];0.81[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2183081	GCH1	cis	lymphoblastoid	seeQTL
rs2183081	KTN1	cis	cerebellum	SCAN
rs2183081	ATG14	cis	cerebellum	SCAN
rs2183081	FBXO34	cis	cerebellum	SCAN
rs2183081	PELI2	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55303400-55337000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr14:55305200-55337200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:55306200-55337000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr14:55306400-55336800	Weak transcription	Dnd41	blood
5	chr14:55306800-55337000	Weak transcription	Brain Anterior Caudate	brain
6	chr14:55311800-55337000	Weak transcription	Fetal Intestine Large	intestine
7	chr14:55321000-55337000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:55321200-55337000	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr14:55324800-55337000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr14:55325000-55337200	Weak transcription	Adipose Nuclei	Adipose
11	chr14:55327000-55338200	Weak transcription	Primary B cells from peripheral blood	blood
12	chr14:55329400-55337000	Weak transcription	Fetal Intestine Small	intestine
13	chr14:55329400-55347800	Weak transcription	Primary B cells from cord blood	blood
14	chr14:55329600-55337200	Weak transcription	Stomach Mucosa	stomach
15	chr14:55330800-55337200	Weak transcription	Aorta	Aorta
16	chr14:55330800-55347800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr14:55331400-55337000	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr14:55331600-55337200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr14:55331800-55344800	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr14:55331800-55347600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr14:55332800-55338000	Weak transcription	Small Intestine	intestine
22	chr14:55333200-55343800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:55333600-55337000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr14:55333600-55337000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr14:55333600-55337000	Weak transcription	Lung	lung
26	chr14:55333800-55337000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr14:55333800-55337000	Weak transcription	NHLF	lung
28	chr14:55334000-55337000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr14:55334000-55337000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr14:55334000-55337000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr14:55334000-55346200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr14:55334200-55337000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr14:55334200-55337000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr14:55334200-55337000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr14:55334200-55337000	Weak transcription	Fetal Stomach	stomach
36	chr14:55334200-55337000	Weak transcription	Right Atrium	heart
37	chr14:55334200-55337200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr14:55334400-55337000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr14:55334400-55337200	Weak transcription	Fetal Muscle Trunk	muscle
40	chr14:55334800-55337200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr14:55336000-55337000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr14:55336400-55336800	Enhancers	A549	lung
43	chr14:55336400-55337000	Enhancers	HepG2	liver
44	chr14:55336400-55337200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr14:55336400-55337600	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr14:55336400-55338400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
47	chr14:55336600-55336800	Enhancers	Liver	Liver
48	chr14:55336600-55336800	Enhancers	Duodenum Mucosa	Duodenum
49	chr14:55336600-55336800	Flanking Active TSS	Hela-S3	cervix
50	chr14:55336600-55337000	Enhancers	HUES6 Cell Line	embryonic stem cell

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