Variant report

Variant	rs11552449
Chromosome Location	chr1:114448389-114448390
allele	A/C/G/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	TBP	chr1:114447191-114448525	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr1:114446705-114448409	K562	blood:	n/a	chr1:114447122-114447131
3	ZKSCAN1	chr1:114446919-114448391	Hela-S3	cervix:	n/a	n/a
4	MYC	chr1:114446758-114448458	Hela-S3	cervix:	n/a	chr1:114447122-114447131
5	MAFK	chr1:114447005-114448536	K562	blood:	n/a	n/a
6	CHD2	chr1:114446998-114448470	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr1:114446593-114448470	Hela-S3	cervix:	n/a	n/a
8	CEBPB	chr1:114446772-114448431	Hela-S3	cervix:	n/a	n/a
9	YY1	chr1:114448197-114448533	H1-hESC	embryonic stem cell:	n/a	n/a
10	CCNT2	chr1:114446648-114448457	K562	blood:	n/a	n/a
11	PML	chr1:114446940-114448489	K562	blood:	n/a	n/a
12	RAD21	chr1:114447041-114448485	HCT-116	colon:	n/a	chr1:114448017-114448030 chr1:114447872-114447891 chr1:114447996-114448008
13	TCF12	chr1:114447219-114448578	ECC-1	luminal epithelium:	n/a	n/a
14	CEBPB	chr1:114448294-114448828	K562	blood:	n/a	n/a
15	MAX	chr1:114445917-114448671	MCF-7	breast:	n/a	chr1:114448611-114448620 chr1:114447122-114447131
16	POLR2A	chr1:114446876-114448536	GM18526	blood:	n/a	n/a
17	POLR2A	chr1:114446984-114448445	Hela-S3	cervix:	n/a	n/a
18	MXI1	chr1:114446060-114448767	SK-N-SH	brain:	n/a	n/a
19	ZBTB7A	chr1:114448024-114448612	ECC-1	luminal epithelium:	n/a	n/a
20	SIN3A	chr1:114446851-114448628	H1-hESC	embryonic stem cell:	n/a	chr1:114447859-114447872 chr1:114447865-114447876
21	NR2F2	chr1:114446295-114448569	K562	blood:	n/a	n/a
22	ELF1	chr1:114447068-114448462	GM12878	blood:	n/a	n/a
23	POLR2A	chr1:114446618-114448634	SK-N-MC	brain:	n/a	n/a
24	POLR2A	chr1:114446739-114448602	HL-60	blood:	n/a	n/a
25	JUND	chr1:114446322-114448706	MCF-7	breast:	n/a	chr1:114447429-114447440 chr1:114446687-114446701
26	MAX	chr1:114446748-114448488	Hela-S3	cervix:	n/a	chr1:114447122-114447131
27	GATA1	chr1:114446471-114448641	PBDE	blood:	n/a	chr1:114447173-114447182
28	ZNF384	chr1:114447257-114448580	GM12878	blood:	n/a	n/a
29	CTCF	chr1:114446821-114448671	SK-N-SH	brain:	n/a	chr1:114447874-114447892 chr1:114447746-114447756 chr1:114447876-114447889 chr1:114447880-114447889 chr1:114447875-114447891 chr1:114448016-114448029
30	JUND	chr1:114447296-114448421	H1-hESC	embryonic stem cell:	n/a	chr1:114447429-114447440
31	MXI1	chr1:114446427-114448753	IMR90	lung:	n/a	n/a
32	HMGN3	chr1:114447231-114448432	K562	blood:	n/a	n/a
33	POLR2A	chr1:114446703-114448588	GM12892	blood:	n/a	n/a
34	E2F4	chr1:114447167-114448412	Hela-S3	cervix:	n/a	n/a
35	RAD21	chr1:114446810-114448468	IMR90	lung:	n/a	chr1:114448017-114448030 chr1:114447872-114447891 chr1:114447996-114448008 chr1:114446812-114446826
36	MTA3	chr1:114447667-114448399	GM12878	blood:	n/a	n/a
37	MAFK	chr1:114446727-114448552	Hela-S3	cervix:	n/a	n/a
38	ZNF143	chr1:114447105-114448539	H1-hESC	embryonic stem cell:	n/a	n/a
39	REST	chr1:114446713-114448515	H1-neurons	neurons:	n/a	chr1:114447859-114447872
40	MAX	chr1:114446598-114448548	K562	blood:	n/a	chr1:114447122-114447131
41	MXI1	chr1:114446918-114448495	H1-hESC	embryonic stem cell:	n/a	n/a
42	MAX	chr1:114446648-114448503	NB4	blood:	n/a	chr1:114447122-114447131
43	SRF	chr1:114446421-114448761	MCF-7	breast:	n/a	n/a
44	HCFC1	chr1:114446741-114448776	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr1:114446320-114448436	GM19099	blood:	n/a	n/a
46	MAZ	chr1:114446539-114448565	IMR90	lung:	n/a	chr1:114447122-114447131
47	ELK1	chr1:114447170-114448429	Hela-S3	cervix:	n/a	n/a
48	MXI1	chr1:114446520-114448501	GM12878	blood:	n/a	n/a
49	MYC	chr1:114446760-114448714	A549	lung:	n/a	chr1:114448611-114448620 chr1:114447122-114447131
50	SRF	chr1:114446565-114448766	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:114447837..114448427-chr1:151583823..151584662,2	Hela-S3	cervix:
2	chr1:114445859..114448805-chr17:42295421..42298283,3	MCF-7	breast:
3	chr1:113257309..113258998-chr1:114446539..114449479,2	K562	blood:
4	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
5	chr1:114446374..114449379-chr1:115298741..115300876,3	MCF-7	breast:
6	chr1:114444168..114452207-chr1:114466193..114476714,61	K562	blood:
7	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
8	chr1:114445068..114448942-chr1:115050232..115055017,4	MCF-7	breast:
9	chr1:114447396..114448619-chr1:114471602..114472886,11	MCF-7	breast:
10	chr1:114446165..114448738-chr1:115053730..115055909,2	MCF-7	breast:
11	chr1:114300712..114302958-chr1:114446093..114449659,3	MCF-7	breast:
12	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
13	chr1:114300422..114303875-chr1:114445198..114448512,7	MCF-7	breast:
14	chr1:114353620..114357151-chr1:114445438..114449458,6	K562	blood:
15	chr1:114300393..114302237-chr1:114446494..114449478,3	K562	blood:
16	chr1:114447832..114448433-chr1:114472824..114473410,2	Hela-S3	cervix:
17	chr1:114363592..114366555-chr1:114447214..114449427,2	MCF-7	breast:
18	chr1:114447452..114448400-chr1:114471566..114472757,4	Hela-S3	cervix:
19	chr1:114447178..114448996-chr1:114471115..114472973,22	MCF-7	breast:

Variant related genes	Relation type
AP4B1	TF binding region
ENSG00000081019	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000163349	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000108312	Chromatin interaction
ENSG00000261595	Chromatin interaction
ENSG00000197323	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs11102694	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11102701	0.91[EUR][1000 genomes]
rs11102702	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12046289	0.85[AMR][1000 genomes]
rs2358994	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2358995	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3761936	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7513707	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Breast cancer	23535729	GWAS catalog

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114445600-114449800	Active TSS	GM12878-XiMat	blood
2	chr1:114446200-114448800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr1:114446200-114449000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr1:114446200-114449600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr1:114446400-114448600	Active TSS	Aorta	Aorta
6	chr1:114446400-114448600	Active TSS	Psoas Muscle	Psoas
7	chr1:114446400-114448600	Active TSS	Right Atrium	heart
8	chr1:114446400-114449200	Active TSS	A549	lung
9	chr1:114446400-114449600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:114446600-114448600	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:114446600-114448600	Active TSS	Esophagus	oesophagus
12	chr1:114446600-114448600	Active TSS	Pancreas	Pancrea
13	chr1:114446600-114448800	Active TSS	NHDF-Ad	bronchial
14	chr1:114446600-114449400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:114446800-114448400	Active TSS	Spleen	Spleen
16	chr1:114446800-114448600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr1:114446800-114448600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:114446800-114448600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr1:114446800-114448600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr1:114446800-114448600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:114446800-114448600	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr1:114446800-114448600	Active TSS	Gastric	stomach
23	chr1:114446800-114448600	Active TSS	Ovary	ovary
24	chr1:114446800-114448600	Active TSS	Small Intestine	intestine
25	chr1:114446800-114448600	Bivalent/Poised TSS	HepG2	liver
26	chr1:114446800-114448800	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:114446800-114448800	Active TSS	HUES64 Cell Line	embryonic stem cell
28	chr1:114446800-114448800	Active TSS	Fetal Stomach	stomach
29	chr1:114446800-114449000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr1:114446800-114449000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:114446800-114449000	Active TSS	NHLF	lung
32	chr1:114447000-114448400	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr1:114447000-114448400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:114447000-114448400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
35	chr1:114447000-114448400	Active TSS	Brain Anterior Caudate	brain
36	chr1:114447000-114448400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr1:114447000-114448400	Active TSS	Brain Substantia Nigra	brain
38	chr1:114447000-114448400	Active TSS	Fetal Brain Male	brain
39	chr1:114447000-114448400	Active TSS	Fetal Intestine Small	intestine
40	chr1:114447000-114448400	Active TSS	Fetal Lung	lung
41	chr1:114447000-114448400	Active TSS	Stomach Mucosa	stomach
42	chr1:114447000-114448600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
43	chr1:114447000-114448600	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:114447000-114448600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:114447000-114448600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr1:114447000-114448600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:114447000-114448600	Active TSS	Brain Angular Gyrus	brain
48	chr1:114447000-114448600	Active TSS	Fetal Heart	heart
49	chr1:114447000-114448800	Active TSS	HUES6 Cell Line	embryonic stem cell
50	chr1:114447000-114448800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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