Variant report

Variant	rs11588956
Chromosome Location	chr1:45096760-45096761
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:31)
CpG islands
(count:61)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:31 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr1:45096374-45097760	K562	blood:	n/a	chr1:45097595-45097610
2	POLR2A	chr1:45096740-45098410	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:45096631-45100261	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:45096755-45098744	K562	blood:	n/a	n/a
5	POLR2A	chr1:45096207-45100173	GM12878	blood:	n/a	n/a
6	POLR2A	chr1:45096750-45098326	GM12892	blood:	n/a	n/a
7	HEY1	chr1:45096599-45099431	K562	blood:	n/a	chr1:45097424-45097439 chr1:45097387-45097402 chr1:45097393-45097408
8	HCFC1	chr1:45096487-45098531	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr1:45096720-45098351	GM12891	blood:	n/a	n/a
10	POLR2A	chr1:45096673-45098518	U87	brain:	n/a	n/a
11	ZC3H11A	chr1:45096665-45097100	K562	blood:	n/a	n/a
12	WRNIP1	chr1:45096617-45097270	GM12878	blood:	n/a	n/a
13	TEAD4	chr1:45096654-45097842	K562	blood:	n/a	n/a
14	POLR2A	chr1:45096696-45098217	GM12891	blood:	n/a	n/a
15	MTA3	chr1:45096515-45098047	GM12878	blood:	n/a	n/a
16	POLR2A	chr1:45096693-45098066	GM12891	blood:	n/a	n/a
17	POLR2A	chr1:45096614-45098490	GM12892	blood:	n/a	n/a
18	POLR2A	chr1:45096599-45099881	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:45096570-45100273	GM12878	blood:	n/a	n/a
20	RCOR1	chr1:45093921-45098862	IMR90	lung:	n/a	n/a
21	POLR2A	chr1:45096644-45099005	K562	blood:	n/a	n/a
22	POLR2A	chr1:45096649-45096852	GM12878	blood:	n/a	n/a
23	CBX3	chr1:45096665-45097743	K562	blood:	n/a	n/a
24	POLR2A	chr1:45096632-45098479	GM12892	blood:	n/a	n/a
25	POLR2A	chr1:45096667-45098756	PANC-1	pancreas:	n/a	n/a
26	TBL1XR1	chr1:45096606-45097912	K562	blood:	n/a	n/a
27	POLR2A	chr1:45096694-45098506	SK-N-MC	brain:	n/a	n/a
28	POLR2A	chr1:45096731-45098345	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:45096576-45098323	ECC-1	luminal epithelium:	n/a	n/a
30	POLR2A	chr1:45096749-45098877	K562	blood:	n/a	n/a
31	POLR2A	chr1:45096735-45098568	PFSK-1	brain:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:45096728-45096778	MCF10A-Er-Src	breast:	n/a
2	chr1:45096728-45096778	RPTEC	kidney:	n/a
3	chr1:45096728-45096778	HRPEpiC	eye:	n/a
4	chr1:45096728-45096778	PrEC	prostate:	n/a
5	chr1:45096728-45096778	Hela-S3	cervix:	n/a
6	chr1:45096728-45096778	A549	lung:	n/a
7	chr1:45096728-45096778	HCPEpiC	choroid plexus:	n/a
8	chr1:45096728-45096778	HCT-116	colon:	n/a
9	chr1:45096728-45096778	GM12892	blood:	n/a
10	chr1:45096728-45096778	BE2_C	brain:	n/a
11	chr1:45096728-45096778	T-47D	breast:	n/a
12	chr1:45096728-45096778	GM19239	blood:	n/a
13	chr1:45096728-45096778	HEEpiC	esophagus:	n/a
14	chr1:45096728-45096778	HMEC	breast:	n/a
15	chr1:45096728-45096778	ovcar-3	ovarian:	n/a
16	chr1:45096728-45096778	HIPEpiC	eye:	n/a
17	chr1:45096728-45096778	SK-N-MC	brain:	n/a
18	chr1:45096728-45096778	PANC-1	pancreas:	n/a
19	chr1:45096728-45096778	NB4	blood:	n/a
20	chr1:45096728-45096778	Hepatocyte	liver:	n/a
21	chr1:45096728-45096778	HL-60	blood:	n/a
22	chr1:45096728-45096778	AoSMC	blood vessel:	n/a
23	chr1:45096728-45096778	H1-hESC	embryonic stem cell:	embryo
24	chr1:45096728-45096778	GM12878	blood:	n/a
25	chr1:45096728-45096778	HepG2	liver:	n/a
26	chr1:45096728-45096778	Jurkat	blood:	n/a
27	chr1:45096728-45096778	SKMC	muscle:	n/a
28	chr1:45096728-45096778	NHDF-neo	bronchial:	n/a
29	chr1:45096728-45096778	LNCaP	prostate:	n/a
30	chr1:45096728-45096778	GM12891	blood:	n/a
31	chr1:45096728-45096778	SAEC	small airway:	n/a
32	chr1:45096728-45096778	NHBE	bronchial:	n/a
33	chr1:45096728-45096778	HNPCEpiC	eye:	n/a
34	chr1:45096728-45096778	HCM	heart:	n/a
35	chr1:45096728-45096778	ProgFib	skin:	n/a
36	chr1:45096728-45096778	AG04450	lung:	fetal
37	chr1:45096728-45096778	HPAEpiC	pulmonary alveolar:	n/a
38	chr1:45096728-45096778	HAEpiC	amniotic membrane:	n/a
39	chr1:45096728-45096778	NT2-D1	testis:	n/a
40	chr1:45096728-45096778	AG09309	skin:	n/a
41	chr1:45096728-45096778	Caco-2	colon:	n/a
42	chr1:45096728-45096778	AG04449	skin:	fetal
43	chr1:45096728-45096778	HRE	kidney:	n/a
44	chr1:45096728-45096778	IMR90	lung:	fetal
45	chr1:45096728-45096778	ECC-1	luminal epithelium:	n/a
46	chr1:45096728-45096778	AG09319	gingival:	n/a
47	chr1:45096728-45096778	U87	brain:	n/a
48	chr1:45096728-45096778	CMK	blood:	n/a
49	chr1:45096728-45096778	K562	blood:	n/a
50	chr1:45096728-45096778	BJ	skin:	n/a

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:44818922..44822604-chr1:45096121..45099112,6	K562	blood:
2	chr1:45089432..45094163-chr1:45095736..45099125,6	MCF-7	breast:
3	chr1:44677773..44680547-chr1:45095385..45099072,4	K562	blood:
4	chr1:45077147..45081258-chr1:45096476..45100107,4	MCF-7	breast:
5	chr1:45096334..45100885-chr1:45195106..45197628,6	K562	blood:
6	chr1:45095169..45100377-chr1:45133934..45142864,15	K562	blood:
7	chr1:45095364..45099259-chr1:45185766..45189852,13	K562	blood:
8	chr1:45096334..45099417-chr1:45195073..45197438,5	K562	blood:
9	chr1:45096184..45099066-chr1:45264568..45266380,3	K562	blood:
10	chr1:45086647..45106769-chr1:45179099..45192041,56	K562	blood:
11	chr1:45051849..45053627-chr1:45094986..45097347,2	K562	blood:
12	chr1:44440424..44442164-chr1:45096404..45098062,2	K562	blood:
13	chr1:45096002..45100159-chr1:45110119..45116077,6	MCF-7	breast:
14	chr1:45096122..45099489-chr1:45284877..45287072,3	K562	blood:

No data

Variant related genes	Relation type
RNF220	TF binding region
RNF220	CpG island
ENSG00000117419	Chromatin interaction
ENSG00000198520	Chromatin interaction
ENSG00000126106	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000199377	Chromatin interaction
ENSG00000178028	Chromatin interaction
ENSG00000117410	Chromatin interaction
ENSG00000200169	Chromatin interaction
ENSG00000187147	Chromatin interaction
ENSG00000173846	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1051664	0.92[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];0.88[TSI][hapmap];0.93[EUR][1000 genomes]
rs11581074	1.00[CHB][hapmap]
rs11584765	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2236219	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2355365	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs28453885	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3444	0.82[TSI][hapmap]
rs3768439	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs3850853	0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.80[MEX][hapmap]
rs4660284	0.84[TSI][hapmap];0.81[EUR][1000 genomes]
rs4660285	0.82[EUR][1000 genomes]
rs4660818	0.84[CHD][hapmap]
rs4660821	0.84[CHD][hapmap]
rs6429544	0.92[CHB][hapmap]
rs6667593	0.92[CHB][hapmap]
rs6683133	0.88[CHD][hapmap]
rs72671954	0.81[EUR][1000 genomes]
rs7538419	0.88[CHD][hapmap]
rs7539312	1.00[CHB][hapmap]
rs995089	0.82[GIH][hapmap];0.84[TSI][hapmap];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533037	chr1:44361728-45333408	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	469 gene(s)	inside rSNPs	diseases
2	nsv1004861	chr1:44843654-45210176	Flanking Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
3	nsv534940	chr1:44843654-45210176	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	346 gene(s)	inside rSNPs	diseases
4	nsv461395	chr1:44898998-45119965	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
5	nsv546144	chr1:44898998-45119965	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
6	nsv998476	chr1:45001278-45311757	Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases
7	nsv534941	chr1:45001278-45311757	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	426 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45074800-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr1:45079600-45096800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr1:45083000-45097000	Weak transcription	Spleen	Spleen
4	chr1:45083400-45097200	Weak transcription	Gastric	stomach
5	chr1:45083600-45097000	Weak transcription	Right Atrium	heart
6	chr1:45084200-45097000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr1:45084800-45096800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr1:45085600-45097000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr1:45085600-45097000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:45085800-45096800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr1:45087200-45096800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:45087800-45096800	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr1:45089800-45097000	Weak transcription	Psoas Muscle	Psoas
14	chr1:45090800-45096800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:45091400-45097000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr1:45091400-45097000	Weak transcription	Fetal Muscle Trunk	muscle
17	chr1:45091800-45097000	Weak transcription	Fetal Brain Female	brain
18	chr1:45092000-45096800	Weak transcription	Fetal Brain Male	brain
19	chr1:45092000-45097000	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr1:45093200-45097000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr1:45093600-45097200	Enhancers	NHLF	lung
22	chr1:45093800-45097200	Enhancers	NHDF-Ad	bronchial
23	chr1:45094000-45096800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr1:45094000-45096800	Weak transcription	Primary B cells from cord blood	blood
25	chr1:45094000-45097000	Enhancers	Osteobl	bone
26	chr1:45094200-45097000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
27	chr1:45094600-45096800	Weak transcription	Hela-S3	cervix
28	chr1:45094800-45097000	Weak transcription	HMEC	breast
29	chr1:45095400-45097000	Weak transcription	NHEK	skin
30	chr1:45095600-45096800	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr1:45095600-45097000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:45095600-45097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr1:45095600-45097000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:45095800-45096800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr1:45095800-45097000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:45095800-45097000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:45096200-45097000	Genic enhancers	Brain Hippocampus Middle	brain
38	chr1:45096200-45097000	Weak transcription	NH-A	brain
39	chr1:45096200-45097200	Enhancers	Brain Substantia Nigra	brain
40	chr1:45096400-45096800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr1:45096400-45096800	Genic enhancers	Brain Cingulate Gyrus	brain
42	chr1:45096400-45097000	Enhancers	Brain Anterior Caudate	brain
43	chr1:45096400-45097000	Enhancers	HepG2	liver
44	chr1:45096400-45097000	Enhancers	HSMM	muscle
45	chr1:45096400-45097200	Weak transcription	Lung	lung
46	chr1:45096600-45096800	Genic enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:45096600-45096800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:45096600-45096800	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr1:45096600-45096800	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr1:45096600-45096800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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