Variant report

Variant	rs883081
Chromosome Location	chr14:65880621-65880622
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:65685385..65700060-chr14:65874568..65884730,76	MCF-7	breast:
2	chr14:65745595..65748280-chr14:65878483..65880878,2	MCF-7	breast:
3	chr14:65569137..65571197-chr14:65878383..65880649,2	MCF-7	breast:
4	chr14:65880600..65882625-chr14:65890707..65892397,2	MCF-7	breast:
5	chr14:65880088..65881939-chr14:66282983..66284508,2	MCF-7	breast:
6	chr14:65769045..65770910-chr14:65878599..65880667,2	MCF-7	breast:
7	chr14:65879676..65881204-chr14:65933662..65936142,2	MCF-7	breast:
8	chr14:65682951..65699539-chr14:65874873..65882779,51	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258760	Chromatin interaction
ENSG00000259078	Chromatin interaction
ENSG00000125952	Chromatin interaction
ENSG00000255002	Chromatin interaction
ENSG00000180662	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10138570	0.93[CEU][hapmap]
rs10483780	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11158592	0.88[CEU][hapmap]
rs11158593	0.93[CEU][hapmap];0.80[MEX][hapmap]
rs11158596	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11158601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11158602	0.93[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11620749	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11621680	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11622014	0.83[EUR][1000 genomes]
rs11627084	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11628196	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851576	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12589698	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12879202	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12879805	0.80[EUR][1000 genomes]
rs12879971	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12882269	1.00[CHB][hapmap];0.87[ASN][1000 genomes]
rs12883815	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12886334	0.81[EUR][1000 genomes]
rs12887134	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12889002	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12890123	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12890978	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12892058	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12895074	0.86[EUR][1000 genomes]
rs1815654	0.91[ASN][1000 genomes]
rs1953416	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1958561	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2002692	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2149841	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2184603	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2411355	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2411357	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2411816	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2411822	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3783709	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3825640	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4456409	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4581615	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4899179	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4902400	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4902407	0.80[ASN][1000 genomes]
rs67071794	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7146742	0.82[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7153297	0.85[EUR][1000 genomes]
rs7154536	0.82[ASN][1000 genomes]
rs7155541	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs7161123	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs743085	0.82[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.91[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8005710	0.80[ASN][1000 genomes]
rs8012278	0.82[EUR][1000 genomes]
rs867972	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs883082	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832818	chr14:65706859-65882320	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1036403	chr14:65724229-66208114	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
3	nsv1043943	chr14:65782466-66698411	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
4	nsv542120	chr14:65782466-66698411	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv1039168	chr14:65811750-66308343	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
6	nsv510639	chr14:65853883-65884315	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	esv3404983	chr14:65878424-65881572	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs883081	VTI1B	cis	parietal	SCAN
rs883081	HIF1A	cis	cerebellum	SCAN
rs883081	FUT8	cis	cerebellum	SCAN

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:65877600-65882200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:65877600-65885400	Active TSS	GM12878-XiMat	blood
3	chr14:65877800-65881000	Active TSS	Fetal Intestine Small	intestine
4	chr14:65877800-65881600	Active TSS	Rectal Mucosa Donor 29	rectum
5	chr14:65877800-65882600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr14:65878000-65880800	Active TSS	Placenta	Placenta
7	chr14:65878000-65880800	Active TSS	Right Atrium	heart
8	chr14:65878000-65881000	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr14:65878000-65881000	Active TSS	Fetal Kidney	kidney
10	chr14:65878000-65881000	Active TSS	HSMMtube	muscle
11	chr14:65878000-65881200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:65878000-65881400	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr14:65878000-65881800	Active TSS	Brain Angular Gyrus	brain
14	chr14:65878000-65881800	Active TSS	Fetal Intestine Large	intestine
15	chr14:65878000-65882400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr14:65878200-65880800	Active TSS	H9 Cell Line	embryonic stem cell
17	chr14:65878200-65880800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr14:65878200-65880800	Active TSS	Brain Substantia Nigra	brain
19	chr14:65878200-65880800	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr14:65878200-65880800	Active TSS	Esophagus	oesophagus
21	chr14:65878200-65880800	Active TSS	Ovary	ovary
22	chr14:65878200-65880800	Active TSS	Placenta Amnion	Placenta Amnion
23	chr14:65878200-65880800	Active TSS	Psoas Muscle	Psoas
24	chr14:65878200-65880800	Active TSS	Stomach Mucosa	stomach
25	chr14:65878200-65880800	Active TSS	HepG2	liver
26	chr14:65878200-65880800	Active TSS	NHDF-Ad	bronchial
27	chr14:65878200-65881000	Active TSS	H1 Cell Line	embryonic stem cell
28	chr14:65878200-65881000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr14:65878200-65881000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr14:65878200-65881000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:65878200-65881000	Active TSS	Brain Anterior Caudate	brain
32	chr14:65878200-65881000	Active TSS	Pancreatic Islets	Pancreatic Islet
33	chr14:65878200-65881200	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr14:65878200-65881400	Active TSS	Duodenum Mucosa	Duodenum
35	chr14:65878200-65881600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
36	chr14:65878200-65881800	Active TSS	Brain Hippocampus Middle	brain
37	chr14:65878400-65880800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr14:65878400-65880800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr14:65878400-65880800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr14:65878400-65880800	Active TSS	Primary T helper naive cells from peripheral blood	blood
41	chr14:65878400-65880800	Active TSS	Rectal Mucosa Donor 31	rectum
42	chr14:65878400-65881000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr14:65878400-65881200	Active TSS	iPS-15b Cell Line	embryonic stem cell
44	chr14:65878400-65881200	Active TSS	Brain Cingulate Gyrus	brain
45	chr14:65878400-65881600	Active TSS	HUES6 Cell Line	embryonic stem cell
46	chr14:65878400-65881600	Active TSS	Brain Inferior Temporal Lobe	brain
47	chr14:65878400-65881800	Active TSS	iPS-20b Cell Line	embryonic stem cell
48	chr14:65878600-65880800	Active TSS	Gastric	stomach
49	chr14:65878600-65881000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr14:65878600-65881000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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