Variant report

Variant	rs12891489
Chromosome Location	chr14:56079865-56079866
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	chr14:56046559..56049206-chr14:56078372..56080917,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000186615	Chromatin interaction
ENSG00000126777	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10136386	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs10136408	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10483644	0.86[CEU][hapmap]
rs10483649	0.85[CEU][hapmap]
rs12432887	0.86[CEU][hapmap]
rs12435643	0.86[CEU][hapmap]
rs12590388	0.86[CEU][hapmap]
rs12590936	0.85[CEU][hapmap]
rs12888809	0.85[CEU][hapmap]
rs17128614	0.85[CEU][hapmap]
rs17128657	0.86[CEU][hapmap]
rs17128684	0.86[CEU][hapmap]
rs1951889	0.86[CEU][hapmap]
rs1951890	0.80[CEU][hapmap]
rs2252189	0.86[CEU][hapmap]
rs2274076	0.86[CEU][hapmap]
rs2274078	0.86[CEU][hapmap]
rs34872770	0.91[ASN][1000 genomes]
rs3736877	0.82[JPT][hapmap]
rs3783654	0.82[JPT][hapmap]
rs4901592	0.86[ASN][1000 genomes]
rs4901593	0.88[ASN][1000 genomes]
rs7156566	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	nsv901965	chr14:55976428-56101879	Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12891489	KTN1	cis	cerebellum	SCAN
rs12891489	KTN1	cis	parietal	SCAN
rs12891489	CNIH	cis	cerebellum	SCAN
rs12891489	GCH1	cis	cerebellum	SCAN
rs12891489	GCH1	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:56048400-56086000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:56052000-56080200	Weak transcription	Primary T cells fromperipheralblood	blood
3	chr14:56061000-56085400	Weak transcription	Fetal Kidney	kidney
4	chr14:56061000-56085400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr14:56061200-56082400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr14:56064200-56082800	Weak transcription	Stomach Smooth Muscle	stomach
7	chr14:56066600-56086200	Weak transcription	Fetal Intestine Small	intestine
8	chr14:56066600-56086200	Weak transcription	Gastric	stomach
9	chr14:56066800-56080000	Weak transcription	Fetal Muscle Leg	muscle
10	chr14:56066800-56086200	Weak transcription	Fetal Stomach	stomach
11	chr14:56067600-56080600	Weak transcription	GM12878-XiMat	blood
12	chr14:56067800-56082200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr14:56068000-56081400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr14:56068600-56080400	Weak transcription	Fetal Muscle Trunk	muscle
15	chr14:56068600-56086200	Weak transcription	Spleen	Spleen
16	chr14:56068600-56086600	Weak transcription	Lung	lung
17	chr14:56068800-56080600	Weak transcription	Esophagus	oesophagus
18	chr14:56068800-56081000	Weak transcription	Liver	Liver
19	chr14:56069600-56086800	Weak transcription	Pancreas	Pancrea
20	chr14:56070400-56086200	Weak transcription	Aorta	Aorta
21	chr14:56070800-56083000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr14:56070800-56085000	Weak transcription	Colon Smooth Muscle	Colon
23	chr14:56071000-56081200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr14:56071000-56083600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr14:56071000-56086000	Weak transcription	Thymus	Thymus
26	chr14:56071800-56086200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr14:56072400-56086200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:56073200-56080600	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr14:56073200-56081200	Weak transcription	Adipose Nuclei	Adipose
30	chr14:56073200-56082800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr14:56074600-56080200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr14:56074600-56081200	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr14:56074600-56084600	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr14:56074600-56086000	Weak transcription	Brain Angular Gyrus	brain
35	chr14:56075800-56081600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr14:56076200-56086000	Weak transcription	Small Intestine	intestine
37	chr14:56076400-56085800	Weak transcription	Brain Cingulate Gyrus	brain
38	chr14:56076600-56082600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr14:56076600-56082800	Weak transcription	Fetal Lung	lung
40	chr14:56076600-56083200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr14:56076600-56083400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr14:56076600-56083600	Weak transcription	Brain Anterior Caudate	brain
43	chr14:56076600-56085800	Weak transcription	Ovary	ovary
44	chr14:56076600-56086000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr14:56076600-56086200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr14:56076800-56080200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr14:56076800-56080600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr14:56076800-56082800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr14:56077000-56080000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr14:56077000-56080800	Weak transcription	NHDF-Ad	bronchial

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