Variant report

Variant	rs2667960
Chromosome Location	chr1:220444001-220444002
allele	A/G
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	chr1:220443897-220444644	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:220443180-220446565	GM12891	blood:	n/a	n/a
3	WRNIP1	chr1:220443912-220444515	GM12878	blood:	n/a	n/a
4	JUN	chr1:220443617-220447007	K562	blood:	n/a	chr1:220444866-220444875 chr1:220445240-220445252
5	POLR2A	chr1:220443457-220446239	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:220443810-220446621	MCF10A-Er-Src	breast:	n/a	n/a
7	CHD1	chr1:220443928-220444107	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:220440528..220443413-chr1:220443546..220445862,4	MCF-7	breast:
2	chr1:220443657..220445570-chr1:220960265..220962335,2	MCF-7	breast:

Variant related genes	Relation type
AURKAPS1	TF binding region
ENSG00000213033	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1033107	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs10495144	1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10863535	0.85[AMR][1000 genomes]
rs11118502	0.85[AMR][1000 genomes]
rs11118505	0.85[AMR][1000 genomes]
rs12062286	0.87[AFR][1000 genomes]
rs12066759	1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12070983	0.85[AMR][1000 genomes]
rs2491268	0.94[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2667961	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2667962	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2667963	1.00[AMR][1000 genomes]
rs2789791	0.85[AMR][1000 genomes]
rs2808010	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2808017	0.86[ASW][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2814493	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4445474	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9431233	0.92[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001681	chr1:220425057-220548325	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	nsv535298	chr1:220425057-220548325	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:220426600-220444400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:220426800-220444200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:220426800-220444400	Weak transcription	Colonic Mucosa	Colon
4	chr1:220426800-220445000	Weak transcription	Aorta	Aorta
5	chr1:220426800-220445000	Weak transcription	Pancreas	Pancrea
6	chr1:220427000-220444200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:220427000-220445000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr1:220434800-220444800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr1:220439400-220444200	Weak transcription	Brain Substantia Nigra	brain
10	chr1:220439400-220444800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:220441400-220444200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:220441400-220444200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr1:220441400-220444200	Weak transcription	Fetal Stomach	stomach
14	chr1:220441800-220444200	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr1:220441800-220444800	Enhancers	Small Intestine	intestine
16	chr1:220442000-220444200	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr1:220442000-220444200	Weak transcription	Placenta	Placenta
18	chr1:220442000-220444800	Weak transcription	Fetal Muscle Trunk	muscle
19	chr1:220442400-220444200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr1:220442400-220444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr1:220442400-220444200	Enhancers	Adipose Nuclei	Adipose
22	chr1:220442400-220444400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:220442400-220444400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:220442600-220444200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:220442600-220444200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr1:220442600-220444200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr1:220442600-220444400	Enhancers	Primary T cells fromperipheralblood	blood
28	chr1:220442600-220444800	Enhancers	Liver	Liver
29	chr1:220442800-220444200	Weak transcription	Fetal Muscle Leg	muscle
30	chr1:220443000-220444200	Enhancers	Colon Smooth Muscle	Colon
31	chr1:220443200-220444200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr1:220443200-220444200	Enhancers	Thymus	Thymus
33	chr1:220443200-220444400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr1:220443200-220444400	Enhancers	Fetal Intestine Large	intestine
35	chr1:220443200-220444400	Transcr. at gene 5' and 3'	Dnd41	blood
36	chr1:220443200-220444800	Enhancers	Primary B cells from peripheral blood	blood
37	chr1:220443200-220444800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr1:220443200-220445000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr1:220443400-220444200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr1:220443400-220444200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr1:220443400-220444200	Enhancers	Brain Cingulate Gyrus	brain
42	chr1:220443400-220444200	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr1:220443400-220444200	Enhancers	Stomach Smooth Muscle	stomach
44	chr1:220443400-220444200	Genic enhancers	HSMM	muscle
45	chr1:220443400-220444200	Enhancers	HSMMtube	muscle
46	chr1:220443400-220444200	Enhancers	HUVEC	blood vessel
47	chr1:220443400-220444200	Enhancers	Monocytes-CD14+_RO01746	blood
48	chr1:220443400-220444400	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr1:220443400-220444400	Transcr. at gene 5' and 3'	K562	blood
50	chr1:220443400-220444600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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