Variant report

Variant	rs17124345
Chromosome Location	chr1:85726103-85726104
allele	C/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	POLR2A	chr1:85724115-85729465	PANC-1	pancreas:	n/a	n/a
2	SMC3	chr1:85724888-85726141	SK-N-SH	brain:	n/a	chr1:85724969-85724983 chr1:85725437-85725447 chr1:85725437-85725451
3	POLR2A	chr1:85725091-85726766	IMR90	lung:	n/a	n/a
4	CTCF	chr1:85725980-85726130	AG10803	skin:	n/a	n/a
5	MAZ	chr1:85724131-85726510	IMR90	lung:	n/a	chr1:85725758-85725767 chr1:85724906-85724916
6	POLR2A	chr1:85724881-85726215	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:85725007-85726450	MCF10A-Er-Src	breast:	n/a	n/a
8	HCFC1	chr1:85724873-85726105	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:85726071..85727906-chr1:85736264..85738614,2	K562	blood:
2	chr1:85722628..85726570-chr1:85740869..85744448,4	MCF-7	breast:
3	chr1:85724038..85728124-chr1:85728267..85730109,3	K562	blood:
4	chr1:85723982..85727421-chr1:85728589..85731374,3	MCF-7	breast:
5	chr1:85725564..85729269-chr1:85738227..85742428,6	MCF-7	breast:
6	chr1:85723214..85729954-chr1:85738689..85743771,11	K562	blood:
7	chr1:85664620..85668785-chr1:85722586..85726821,6	MCF-7	breast:

Variant related genes	Relation type
C1orf52	TF binding region
ENSG00000223254	TF binding region
ENSG00000142867	Chromatin interaction
ENSG00000223653	Chromatin interaction
ENSG00000097096	Chromatin interaction
ENSG00000223254	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1060843	0.93[CHB][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs11161564	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11161581	0.93[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs11161583	0.92[ASN][1000 genomes]
rs12065528	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12066982	0.89[ASN][1000 genomes]
rs12068389	0.89[ASN][1000 genomes]
rs12068788	0.93[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs12084232	0.89[ASN][1000 genomes]
rs12086970	0.89[ASN][1000 genomes]
rs12087340	0.93[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12563515	0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12726649	0.93[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs12743302	1.00[ASN][1000 genomes]
rs12744565	0.93[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs12746169	0.96[ASN][1000 genomes]
rs35486093	1.00[ASN][1000 genomes]
rs35783363	0.89[ASN][1000 genomes]
rs35798604	1.00[ASN][1000 genomes]
rs36116171	0.96[ASN][1000 genomes]
rs4074156	1.00[CHB][hapmap];0.93[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4258258	1.00[ASN][1000 genomes]
rs6693229	0.89[ASN][1000 genomes]
rs9887811	0.94[ASN][1000 genomes]
rs9887812	0.93[CHB][hapmap];0.90[CHD][hapmap];0.96[GIH][hapmap];0.89[JPT][hapmap];0.92[ASN][1000 genomes]
rs9887879	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006994	chr1:85454304-86327679	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
2	esv34165	chr1:85542040-85846249	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv830459	chr1:85589585-85786311	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:85724000-85726200	Active TSS	Right Atrium	heart
2	chr1:85724400-85726200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr1:85724600-85726200	Active TSS	Duodenum Mucosa	Duodenum
4	chr1:85725400-85726200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:85725400-85726200	Flanking Active TSS	Adipose Nuclei	Adipose
6	chr1:85725400-85726600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:85725400-85726800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:85725400-85728200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr1:85725400-85732200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:85725400-85732200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:85725400-85733200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr1:85725400-85734600	Weak transcription	Small Intestine	intestine
13	chr1:85725400-85741000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:85725600-85726200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr1:85725600-85726200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr1:85725600-85726200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr1:85725600-85726200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
18	chr1:85725600-85726200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
19	chr1:85725600-85726200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
20	chr1:85725600-85726200	Flanking Active TSS	Stomach Smooth Muscle	stomach
21	chr1:85725600-85726400	Flanking Active TSS	Fetal Lung	lung
22	chr1:85725600-85732200	Weak transcription	Thymus	Thymus
23	chr1:85725600-85734600	Weak transcription	Lung	lung
24	chr1:85725600-85737000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:85725800-85726200	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr1:85725800-85726600	Enhancers	Fetal Stomach	stomach
27	chr1:85725800-85726800	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr1:85725800-85728200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr1:85725800-85728400	Weak transcription	Fetal Intestine Large	intestine
30	chr1:85725800-85729200	Weak transcription	Fetal Thymus	thymus
31	chr1:85725800-85729400	Weak transcription	Primary monocytes fromperipheralblood	blood
32	chr1:85725800-85729800	Weak transcription	Primary T cells from cord blood	blood
33	chr1:85725800-85729800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:85725800-85730000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr1:85725800-85730000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr1:85725800-85731600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:85725800-85731600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr1:85725800-85731800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
39	chr1:85725800-85731800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr1:85725800-85732200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr1:85725800-85732200	Weak transcription	Colonic Mucosa	Colon
42	chr1:85725800-85732800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:85725800-85733800	Weak transcription	Brain Germinal Matrix	brain
44	chr1:85725800-85734600	Weak transcription	H9 Cell Line	embryonic stem cell
45	chr1:85725800-85734600	Weak transcription	Esophagus	oesophagus
46	chr1:85725800-85734800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr1:85725800-85739400	Weak transcription	Aorta	Aorta
48	chr1:85726000-85726200	Enhancers	iPS-15b Cell Line	embryonic stem cell
49	chr1:85726000-85726200	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
50	chr1:85726000-85726200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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