Variant report

Variant	rs1467652
Chromosome Location	chr13:111187750-111187751
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	chr13:111100852..111102646-chr13:111187472..111189317,2	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1122092	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11616542	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11619682	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11619777	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1467650	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1467651	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4771689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4773211	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4773212	0.83[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58927807	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7997619	0.89[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7998064	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9515244	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9521822	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9559838	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs998489	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv1046423	chr13:110936104-111286607	Weak transcription Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv832720	chr13:111100235-111295993	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv1046291	chr13:111125747-111257861	Weak transcription Active TSS Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1045143	chr13:111126822-111242791	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
6	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
7	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
8	nsv901010	chr13:111165390-111286592	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
9	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
11	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv901011	chr13:111168951-111280002	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1467652	RAB20	cis	parietal	SCAN
rs1467652	KIAA1614	trans	parietal	SCAN
rs1467652	C13orf35	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111160800-111209600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr13:111167000-111190800	Weak transcription	Fetal Kidney	kidney
3	chr13:111178600-111188000	Weak transcription	Primary B cells from cord blood	blood
4	chr13:111180000-111188000	Weak transcription	Right Ventricle	heart
5	chr13:111180000-111188200	Weak transcription	Brain Anterior Caudate	brain
6	chr13:111180200-111189400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr13:111180400-111189600	Weak transcription	Colonic Mucosa	Colon
8	chr13:111181000-111188000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr13:111181400-111190800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr13:111181800-111187800	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr13:111182000-111188000	Weak transcription	Right Atrium	heart
12	chr13:111182000-111192200	Weak transcription	Fetal Heart	heart
13	chr13:111182200-111188000	Weak transcription	Left Ventricle	heart
14	chr13:111182200-111193400	Weak transcription	Aorta	Aorta
15	chr13:111182400-111189800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr13:111182400-111193800	Weak transcription	HepG2	liver
17	chr13:111182400-111203600	Weak transcription	Brain Substantia Nigra	brain
18	chr13:111183000-111191400	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr13:111183400-111190400	Strong transcription	Fetal Intestine Small	intestine
20	chr13:111183600-111188400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr13:111184000-111193200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr13:111184000-111199600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr13:111184000-111211800	Weak transcription	HMEC	breast
24	chr13:111184200-111187800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr13:111184200-111188000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr13:111184200-111189600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:111184200-111193200	Weak transcription	Duodenum Mucosa	Duodenum
28	chr13:111184200-111196400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr13:111184200-111197000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr13:111184400-111187800	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr13:111184600-111188000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr13:111184600-111209800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr13:111184800-111187800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr13:111185200-111188600	Enhancers	Placenta	Placenta
35	chr13:111185600-111188200	Weak transcription	GM12878-XiMat	blood
36	chr13:111185800-111190400	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
37	chr13:111185800-111191000	Weak transcription	Stomach Mucosa	stomach
38	chr13:111185800-111193600	Weak transcription	Colon Smooth Muscle	Colon
39	chr13:111186200-111188200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr13:111186200-111188800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr13:111186400-111188400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:111186400-111193200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr13:111186600-111188000	Weak transcription	Adipose Nuclei	Adipose
44	chr13:111186600-111192400	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr13:111186800-111187800	Weak transcription	Brain Hippocampus Middle	brain
46	chr13:111186800-111188000	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr13:111186800-111188400	Weak transcription	Gastric	stomach
48	chr13:111186800-111190000	Weak transcription	Ovary	ovary
49	chr13:111186800-111191400	Enhancers	Primary neutrophils fromperipheralblood	blood
50	chr13:111186800-111192200	Weak transcription	Stomach Smooth Muscle	stomach

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