Variant report

Variant	rs12148682
Chromosome Location	chr15:55696532-55696533
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TBL1XR1	chr15:55695620-55696695	K562	blood:	n/a	n/a
2	IRF1	chr15:55695525-55696823	K562	blood:	n/a	n/a
3	IRF1	chr15:55694942-55696907	K562	blood:	n/a	chr15:55696816-55696827 chr15:55695071-55695083 chr15:55695059-55695073
4	CUX1	chr15:55695674-55696895	K562	blood:	n/a	n/a
5	EP300	chr15:55694865-55696606	K562	blood:	n/a	chr15:55695657-55695671 chr15:55695838-55695852
6	STAT3	chr15:55696277-55696594	MCF10A-Er-Src	breast:	n/a	n/a
7	POLR2A	chr15:55695102-55696901	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:55609981..55613646-chr15:55692667..55696745,4	K562	blood:
2	chr15:55609398..55612428-chr15:55693917..55698358,4	K562	blood:
3	chr15:55610040..55612568-chr15:55696345..55698141,2	MCF-7	breast:
4	chr15:55687284..55689317-chr15:55695984..55697982,2	MCF-7	breast:
5	chr15:55686108..55691081-chr15:55692026..55698243,11	K562	blood:
6	chr15:55693271..55696849-chr15:55698845..55702459,5	MCF-7	breast:
7	chr15:55694340..55696767-chr15:55697475..55699670,2	MCF-7	breast:

Variant related genes	Relation type
C15orf65	TF binding region
ENSG00000225973	Chromatin interaction
ENSG00000069943	Chromatin interaction
ENSG00000260916	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000261652	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11071184	0.90[ASN][1000 genomes]
rs11071185	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11071186	0.91[ASN][1000 genomes]
rs11637024	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12324434	1.00[CHB][hapmap];0.90[JPT][hapmap];0.96[ASN][1000 genomes]
rs12900382	0.89[ASN][1000 genomes]
rs12908712	0.92[ASN][1000 genomes]
rs12910693	0.95[ASN][1000 genomes]
rs12913017	0.83[ASN][1000 genomes]
rs1624851	0.89[ASN][1000 genomes]
rs2414415	0.88[ASN][1000 genomes]
rs2439045	0.84[ASN][1000 genomes]
rs2447712	0.82[ASN][1000 genomes]
rs4144134	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs472579	1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs4774210	0.93[ASN][1000 genomes]
rs4774211	0.93[ASN][1000 genomes]
rs4774768	0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs493968	1.00[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs501231	1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs549914	1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[ASN][1000 genomes]
rs593556	0.92[ASN][1000 genomes]
rs600753	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs60229152	0.86[ASN][1000 genomes]
rs606446	0.84[ASN][1000 genomes]
rs646322	0.87[ASN][1000 genomes]
rs6493789	0.84[ASN][1000 genomes]
rs6493791	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs685935	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs691447	0.84[ASN][1000 genomes]
rs692636	0.83[ASN][1000 genomes]
rs7168202	0.81[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7169179	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169948	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7170993	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7174641	0.81[JPT][hapmap]
rs7174810	0.91[ASN][1000 genomes]
rs8042996	0.81[JPT][hapmap]
rs9920450	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
4	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
6	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
9	nsv904243	chr15:55627528-55734158	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv948522	chr15:55639867-56032099	Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats 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	31 gene(s)	inside rSNPs	diseases
11	nsv520799	chr15:55645661-55760522	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
12	nsv1041635	chr15:55658171-55943942	Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
13	nsv904244	chr15:55687969-55770911	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12148682	DYX1C1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55611800-55699400	Weak transcription	Colonic Mucosa	Colon
2	chr15:55637000-55699600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr15:55668200-55699800	Weak transcription	Spleen	Spleen
4	chr15:55676000-55699400	Weak transcription	Brain Cingulate Gyrus	brain
5	chr15:55676400-55697200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:55676400-55699400	Weak transcription	Right Ventricle	heart
7	chr15:55676800-55697600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:55678200-55699400	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr15:55679400-55696800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:55681000-55697400	Weak transcription	Gastric	stomach
11	chr15:55681000-55699200	Weak transcription	Lung	lung
12	chr15:55681000-55699600	Weak transcription	Fetal Stomach	stomach
13	chr15:55681200-55699400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr15:55681800-55699600	Weak transcription	NHLF	lung
15	chr15:55687400-55696800	Weak transcription	Psoas Muscle	Psoas
16	chr15:55687400-55699400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr15:55687400-55699400	Weak transcription	Fetal Brain Female	brain
18	chr15:55687400-55699600	Weak transcription	Left Ventricle	heart
19	chr15:55689800-55699600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:55691600-55696800	Weak transcription	Pancreas	Pancrea
21	chr15:55691800-55699400	Enhancers	Primary monocytes fromperipheralblood	blood
22	chr15:55693800-55696600	Enhancers	Duodenum Mucosa	Duodenum
23	chr15:55693800-55697000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
24	chr15:55694000-55698000	Enhancers	Liver	Liver
25	chr15:55694600-55696600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr15:55694600-55698800	Enhancers	Hela-S3	cervix
27	chr15:55694800-55696600	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr15:55694800-55696800	Flanking Active TSS	GM12878-XiMat	blood
29	chr15:55694800-55697000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:55694800-55697000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:55694800-55697200	Enhancers	HepG2	liver
32	chr15:55694800-55697600	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr15:55694800-55698800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr15:55695000-55696600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:55695000-55696800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr15:55695000-55696800	Enhancers	Pancreatic Islets	Pancreatic Islet
37	chr15:55695000-55697000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:55695000-55697000	Enhancers	Fetal Intestine Large	intestine
39	chr15:55695000-55697200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
40	chr15:55695000-55699400	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr15:55695000-55699600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr15:55695000-55699600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr15:55695200-55696600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr15:55695200-55696600	Enhancers	Stomach Mucosa	stomach
45	chr15:55695200-55696800	Enhancers	Duodenum Smooth Muscle	Duodenum
46	chr15:55695200-55696800	Flanking Active TSS	A549	lung
47	chr15:55695200-55697200	Enhancers	Adipose Nuclei	Adipose
48	chr15:55695200-55699200	Weak transcription	Small Intestine	intestine
49	chr15:55695400-55696600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
50	chr15:55695400-55697000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood

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