Variant report

Variant	rs11156878
Chromosome Location	chr14:35735967-35735968
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:35730609..35736672-chr14:35871862..35876542,13	MCF-7	breast:
2	chr14:35734999..35737663-chr14:35744257..35745770,2	MCF-7	breast:
3	chr14:35734715..35736326-chr14:35737698..35740285,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000100906	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10483452	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs11620737	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11623882	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11624462	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11626113	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[YRI][hapmap]
rs11627958	0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs11628446	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12888766	1.00[YRI][hapmap]
rs1475041	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1712354	1.00[ASW][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[YRI][hapmap]
rs17458312	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1963154	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2057337	1.00[ASW][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs4432181	1.00[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4982263	1.00[ASW][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs55693281	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56380926	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61988266	0.90[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs61988267	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988269	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988270	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988271	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61988276	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61989543	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61989544	0.89[ASN][1000 genomes]
rs61989545	0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs61989546	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61989547	0.90[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6571713	1.00[ASW][hapmap];0.82[MEX][hapmap]
rs7153434	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7155760	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158151	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7158706	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs799493	1.00[ASW][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[YRI][hapmap]
rs8013647	1.00[ASW][hapmap];0.82[MEX][hapmap];0.88[YRI][hapmap]
rs8018597	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8018657	1.00[ASW][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.88[YRI][hapmap]
rs8021880	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv870305	chr14:35488290-35852349	Weak transcription Strong transcription Flanking Active TSS Enhancers 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 target site	50 gene(s)	inside rSNPs	diseases
5	nsv1044515	chr14:35510785-35756317	Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
6	nsv1053604	chr14:35548276-35825805	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
7	nsv1052392	chr14:35563220-35893309	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv542036	chr14:35563220-35893309	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	esv2754534	chr14:35690978-35744839	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1038396	chr14:35714499-35788189	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1045288	chr14:35735886-35788189	Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11156878	KIAA0391	cis	Liver	GTEx
rs11156878	RFC1	trans	cerebellum	SCAN
rs11156878	KIAA0391	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35661000-35736400	Weak transcription	Fetal Intestine Small	intestine
2	chr14:35672000-35742200	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr14:35674800-35737000	Weak transcription	Lung	lung
4	chr14:35684600-35737000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr14:35684600-35760800	Weak transcription	HSMM	muscle
6	chr14:35700200-35738000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr14:35705400-35749800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr14:35706800-35760800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr14:35709800-35753600	Weak transcription	Small Intestine	intestine
10	chr14:35710200-35736000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr14:35711000-35737000	Weak transcription	Aorta	Aorta
12	chr14:35716600-35739200	Weak transcription	Adipose Nuclei	Adipose
13	chr14:35716800-35760600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr14:35716800-35761000	Weak transcription	Spleen	Spleen
15	chr14:35717000-35760800	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr14:35717600-35753800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr14:35718200-35741000	Weak transcription	Fetal Lung	lung
18	chr14:35718800-35736600	Weak transcription	Fetal Stomach	stomach
19	chr14:35720000-35744800	Weak transcription	Fetal Brain Male	brain
20	chr14:35722000-35754000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr14:35722000-35760800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr14:35724200-35736000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
23	chr14:35724200-35739000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr14:35724200-35756400	Weak transcription	Left Ventricle	heart
25	chr14:35724400-35742400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr14:35727000-35736400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:35727200-35741800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr14:35727200-35742400	Weak transcription	Osteobl	bone
29	chr14:35727200-35742600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:35727200-35744200	Weak transcription	Fetal Heart	heart
31	chr14:35727200-35754600	Weak transcription	NHDF-Ad	bronchial
32	chr14:35727200-35756400	Weak transcription	Stomach Mucosa	stomach
33	chr14:35727200-35761000	Weak transcription	NHLF	lung
34	chr14:35727400-35736200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr14:35727400-35739400	Weak transcription	NHEK	skin
36	chr14:35727400-35754000	Weak transcription	HUVEC	blood vessel
37	chr14:35727600-35736000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr14:35727600-35742200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr14:35727600-35743400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr14:35728000-35750200	Weak transcription	Ovary	ovary
41	chr14:35728400-35743200	Weak transcription	Rectal Smooth Muscle	rectum
42	chr14:35728400-35748400	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr14:35728400-35754600	Weak transcription	K562	blood
44	chr14:35728400-35755000	Weak transcription	Colonic Mucosa	Colon
45	chr14:35729800-35739400	Weak transcription	Rectal Mucosa Donor 29	rectum
46	chr14:35729800-35745400	Weak transcription	Brain Angular Gyrus	brain
47	chr14:35730000-35739000	Weak transcription	Pancreas	Pancrea
48	chr14:35730000-35739600	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr14:35730000-35742600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr14:35730000-35747200	Weak transcription	Placenta Amnion	Placenta Amnion

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