Variant report

Variant	rs61827261
Chromosome Location	chr1:170044648-170044649
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:11)
CpG islands
(count:61)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:11 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EBF1	chr1:170044217-170044676	GM12878	blood:	n/a	n/a
2	CUX1	chr1:170043835-170044977	GM12878	blood:	n/a	chr1:170044699-170044713 chr1:170044698-170044707
3	HCFC1	chr1:170042827-170044890	Hela-S3	cervix:	n/a	n/a
4	ATF1	chr1:170044452-170044712	K562	blood:	n/a	n/a
5	EP300	chr1:170044594-170044757	GM12878	blood:	n/a	n/a
6	MXI1	chr1:170042598-170044745	SK-N-SH	brain:	n/a	n/a
7	SMC3	chr1:170043480-170044881	SK-N-SH	brain:	n/a	n/a
8	EBF1	chr1:170042606-170044754	GM12878	blood:	n/a	n/a
9	WRNIP1	chr1:170043091-170044649	GM12878	blood:	n/a	n/a
10	EP300	chr1:170043479-170044687	GM12878	blood:	n/a	n/a
11	TBL1XR1	chr1:170043396-170044697	GM12878	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:170044647-170044697	MCF-7	breast:	n/a
2	chr1:170044647-170044697	GM12878	blood:	n/a
3	chr1:170044647-170044697	HIPEpiC	eye:	n/a
4	chr1:170044647-170044697	HPAEpiC	pulmonary alveolar:	n/a
5	chr1:170044647-170044697	GM12891	blood:	n/a
6	chr1:170044647-170044697	SAEC	small airway:	n/a
7	chr1:170044647-170044697	HCM	heart:	n/a
8	chr1:170044647-170044697	T-47D	breast:	n/a
9	chr1:170044647-170044697	HRCEpiC	kidney:	n/a
10	chr1:170044647-170044697	RPTEC	kidney:	n/a
11	chr1:170044647-170044697	BJ	skin:	n/a
12	chr1:170044647-170044697	SKMC	muscle:	n/a
13	chr1:170044647-170044697	HMEC	breast:	n/a
14	chr1:170044647-170044697	AG09309	skin:	n/a
15	chr1:170044647-170044697	GM06990	blood:	n/a
16	chr1:170044647-170044697	SK-N-SH_RA	brain:	n/a
17	chr1:170044647-170044697	SK-N-SH	brain:	n/a
18	chr1:170044647-170044697	HCF	heart:	n/a
19	chr1:170044647-170044697	AG04450	lung:	fetal
20	chr1:170044647-170044697	A549	lung:	n/a
21	chr1:170044647-170044697	HCPEpiC	choroid plexus:	n/a
22	chr1:170044647-170044697	GM12892	blood:	n/a
23	chr1:170044647-170044697	ovcar-3	ovarian:	n/a
24	chr1:170044647-170044697	Hepatocyte	liver:	n/a
25	chr1:170044647-170044697	PrEC	prostate:	n/a
26	chr1:170044647-170044697	NHDF-neo	bronchial:	n/a
27	chr1:170044647-170044697	CMK	blood:	n/a
28	chr1:170044647-170044697	K562	blood:	n/a
29	chr1:170044647-170044697	AG04449	skin:	fetal
30	chr1:170044647-170044697	HEEpiC	esophagus:	n/a
31	chr1:170044647-170044697	U87	brain:	n/a
32	chr1:170044647-170044697	IMR90	lung:	fetal
33	chr1:170044647-170044697	LNCaP	prostate:	n/a
34	chr1:170044647-170044697	AG10803	skin:	n/a
35	chr1:170044647-170044697	HNPCEpiC	eye:	n/a
36	chr1:170044647-170044697	PANC-1	pancreas:	n/a
37	chr1:170044647-170044697	NH-A	brain:	n/a
38	chr1:170044647-170044697	SK-N-MC	brain:	n/a
39	chr1:170044647-170044697	AoSMC	blood vessel:	n/a
40	chr1:170044647-170044697	HL-60	blood:	n/a
41	chr1:170044647-170044697	HEK293	kidney:	embryo
42	chr1:170044647-170044697	Caco-2	colon:	n/a
43	chr1:170044647-170044697	AG09319	gingival:	n/a
44	chr1:170044647-170044697	H1-hESC	embryonic stem cell:	embryo
45	chr1:170044647-170044697	MCF10A-Er-Src	breast:	n/a
46	chr1:170044647-170044697	Jurkat	blood:	n/a
47	chr1:170044647-170044697	HepG2	liver:	n/a
48	chr1:170044647-170044697	ECC-1	luminal epithelium:	n/a
49	chr1:170044647-170044697	NT2-D1	testis:	n/a
50	chr1:170044647-170044697	HCT-116	colon:	n/a

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169861326..169864449-chr1:170043806..170046469,4	K562	blood:
2	chr1:170037649..170040302-chr1:170043918..170046865,2	K562	blood:

No data

Variant related genes	Relation type
KIFAP3	TF binding region
KIFAP3	CpG island
ENSG00000075945	Chromatin interaction
ENSG00000000457	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11579254	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11584208	0.82[ASN][1000 genomes]
rs11588736	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs1360294	0.85[AMR][1000 genomes]
rs16862870	0.81[ASN][1000 genomes]
rs16862902	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs16862943	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1928887	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2150111	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4656202	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs4656730	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4656731	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4656732	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs56041446	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs59916635	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61806098	0.81[ASN][1000 genomes]
rs61825320	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61825343	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs61825344	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs61825346	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61825347	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs61825348	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs61825352	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61825353	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs61825354	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61825356	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61825358	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73035088	0.95[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs73041144	0.83[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	nsv1014033	chr1:169968488-170453021	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases
2	nsv535200	chr1:169968488-170453021	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:170043000-170044800	Active TSS	Skeletal Muscle Female	skeletal muscle
2	chr1:170043600-170044800	Active TSS	Colonic Mucosa	Colon
3	chr1:170044000-170044800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr1:170044000-170044800	Flanking Active TSS	Brain Angular Gyrus	brain
5	chr1:170044200-170044800	Flanking Active TSS	Fetal Heart	heart
6	chr1:170044200-170044800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr1:170044200-170044800	Flanking Active TSS	Dnd41	blood
8	chr1:170044200-170045800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:170044200-170051800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:170044400-170044800	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:170044400-170044800	Enhancers	Primary neutrophils fromperipheralblood	blood
12	chr1:170044400-170044800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr1:170044400-170044800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr1:170044400-170044800	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr1:170044400-170044800	Enhancers	Liver	Liver
16	chr1:170044400-170044800	Flanking Active TSS	Brain Anterior Caudate	brain
17	chr1:170044400-170044800	Enhancers	Brain Germinal Matrix	brain
18	chr1:170044400-170044800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr1:170044400-170044800	Enhancers	Fetal Kidney	kidney
20	chr1:170044400-170044800	Flanking Active TSS	HepG2	liver
21	chr1:170044400-170045000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
22	chr1:170044600-170044800	Enhancers	iPS-15b Cell Line	embryonic stem cell
23	chr1:170044600-170044800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:170044600-170044800	Enhancers	Breast Myoepithelial Primary Cells	Breast
25	chr1:170044600-170044800	Enhancers	Primary T cells from cord blood	blood
26	chr1:170044600-170044800	Enhancers	Primary T cells fromperipheralblood	blood
27	chr1:170044600-170044800	Enhancers	Primary T helper cells fromperipheralblood	blood
28	chr1:170044600-170044800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr1:170044600-170044800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr1:170044600-170044800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr1:170044600-170044800	Enhancers	Adipose Nuclei	Adipose
32	chr1:170044600-170044800	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:170044600-170044800	Enhancers	Brain Hippocampus Middle	brain
34	chr1:170044600-170044800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
35	chr1:170044600-170044800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr1:170044600-170044800	Enhancers	Colon Smooth Muscle	Colon
37	chr1:170044600-170044800	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr1:170044600-170044800	Enhancers	Fetal Lung	lung
39	chr1:170044600-170044800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr1:170044600-170044800	Enhancers	GM12878-XiMat	blood
41	chr1:170044600-170044800	Enhancers	Hela-S3	cervix
42	chr1:170044600-170044800	Enhancers	K562	blood
43	chr1:170044600-170045000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr1:170044600-170045000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr1:170044600-170045000	Enhancers	Primary T helper cells PMA-I stimulated	--
46	chr1:170044600-170047800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr1:170044600-170048200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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