Variant report

Variant	rs11806816
Chromosome Location	chr1:154600664-154600665
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	MAX	chr1:154599839-154600766	GM12878	blood:	n/a	chr1:154600500-154600510 chr1:154600500-154600510 chr1:154600499-154600510 chr1:154600498-154600511 chr1:154600500-154600509 chr1:154600498-154600511 chr1:154600499-154600508 chr1:154600499-154600510 chr1:154600500-154600509 chr1:154600498-154600511
2	BCLAF1	chr1:154599882-154600738	GM12878	blood:	n/a	n/a
3	MAX	chr1:154600208-154600772	ECC-1	luminal epithelium:	n/a	chr1:154600500-154600510 chr1:154600500-154600510 chr1:154600499-154600510 chr1:154600498-154600511 chr1:154600500-154600509 chr1:154600498-154600511 chr1:154600499-154600508 chr1:154600499-154600510 chr1:154600500-154600509 chr1:154600498-154600511
4	USF2	chr1:154600317-154600715	K562	blood:	n/a	chr1:154600499-154600510
5	USF1	chr1:154600224-154600730	H1-hESC	embryonic stem cell:	n/a	chr1:154600499-154600510
6	MBD4	chr1:154600359-154600818	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:154599327-154600727	GM12891	blood:	n/a	n/a
8	SRF	chr1:154600137-154600784	MCF-7	breast:	n/a	n/a
9	ELF1	chr1:154600332-154600798	HepG2	liver:	n/a	n/a
10	ETS1	chr1:154600205-154600815	A549	lung:	n/a	chr1:154600689-154600698
11	MAX	chr1:154599457-154601013	A549	lung:	n/a	chr1:154600500-154600510 chr1:154600500-154600510 chr1:154600499-154600510 chr1:154600498-154600511 chr1:154600500-154600509 chr1:154600498-154600511 chr1:154600499-154600508 chr1:154600499-154600510 chr1:154600500-154600509 chr1:154600498-154600511
12	EP300	chr1:154600330-154600756	GM12878	blood:	n/a	n/a
13	FOS	chr1:154600419-154600664	MCF10A-Er-Src	breast:	n/a	n/a
14	CREB1	chr1:154600215-154600692	A549	lung:	n/a	n/a
15	USF1	chr1:154600186-154600807	ECC-1	luminal epithelium:	n/a	chr1:154600499-154600510
16	TBL1XR1	chr1:154600067-154600746	GM12878	blood:	n/a	n/a
17	POLR2A	chr1:154599334-154600692	GM12878	blood:	n/a	n/a
18	IRF1	chr1:154600312-154600716	K562	blood:	n/a	n/a
19	SIN3A	chr1:154599737-154600729	GM12878	blood:	n/a	n/a
20	JUND	chr1:154600312-154600676	HepG2	liver:	n/a	n/a
21	JUND	chr1:154600185-154600757	H1-hESC	embryonic stem cell:	n/a	n/a
22	MXI1	chr1:154599690-154600906	GM12878	blood:	n/a	n/a
23	MXI1	chr1:154599615-154600740	Hela-S3	cervix:	n/a	n/a
24	MYC	chr1:154600259-154600719	HepG2	liver:	n/a	chr1:154600500-154600510 chr1:154600500-154600510 chr1:154600499-154600510 chr1:154600498-154600511 chr1:154600500-154600509 chr1:154600498-154600511 chr1:154600499-154600508 chr1:154600499-154600510 chr1:154600500-154600509 chr1:154600498-154600511
25	POLR2A	chr1:154599665-154600743	GM18951	blood:	n/a	n/a
26	STAT1	chr1:154600397-154600679	GM12878	blood:	n/a	n/a
27	SMC3	chr1:154600540-154600762	HepG2	liver:	n/a	n/a
28	POLR2A	chr1:154599997-154600782	GM12878	blood:	n/a	n/a
29	SIX5	chr1:154600138-154600869	A549	lung:	n/a	n/a
30	USF1	chr1:154600181-154600836	A549	lung:	n/a	chr1:154600499-154600510
31	USF1	chr1:154600262-154600736	SK-N-SH_RA	brain:	n/a	chr1:154600499-154600510
32	CHD1	chr1:154599741-154600775	GM12878	blood:	n/a	chr1:154599956-154599966
33	MAX	chr1:154599996-154600803	H1-hESC	embryonic stem cell:	n/a	chr1:154600500-154600510 chr1:154600500-154600510 chr1:154600499-154600510 chr1:154600498-154600511 chr1:154600500-154600509 chr1:154600498-154600511 chr1:154600499-154600508 chr1:154600499-154600510 chr1:154600500-154600509 chr1:154600498-154600511
34	TBP	chr1:154599529-154600732	K562	blood:	n/a	n/a
35	POLR2A	chr1:154599617-154600726	ProgFib	skin:	n/a	n/a
36	GATA1	chr1:154598852-154602355	K562	blood:	n/a	n/a
37	EP300	chr1:154600228-154600839	A549	lung:	n/a	n/a
38	ATF2	chr1:154600261-154600795	GM12878	blood:	n/a	n/a
39	MAX	chr1:154600294-154600764	A549	lung:	n/a	chr1:154600500-154600510 chr1:154600500-154600510 chr1:154600499-154600510 chr1:154600498-154600511 chr1:154600500-154600509 chr1:154600498-154600511 chr1:154600499-154600508 chr1:154600499-154600510 chr1:154600500-154600509 chr1:154600498-154600511
40	TAF1	chr1:154599858-154600724	ECC-1	luminal epithelium:	n/a	n/a
41	TBP	chr1:154600317-154600852	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:154599288-154600963	H1-hESC	embryonic stem cell:	n/a	n/a
43	PML	chr1:154600345-154600717	GM12878	blood:	n/a	n/a
44	USF1	chr1:154600249-154600750	A549	lung:	n/a	chr1:154600499-154600510
45	POLR2A	chr1:154599745-154600703	H1-hESC	embryonic stem cell:	n/a	n/a
46	CHD2	chr1:154600317-154600692	K562	blood:	n/a	n/a
47	POLR2A	chr1:154599969-154600721	GM12891	blood:	n/a	n/a
48	POLR2A	chr1:154600171-154600710	HepG2	liver:	n/a	n/a
49	ZNF143	chr1:154600320-154600674	K562	blood:	n/a	chr1:154600477-154600495
50	POLR2A	chr1:154599638-154600688	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154530639..154532673-chr1:154599012..154601442,2	K562	blood:
2	chr1:154529929..154534088-chr1:154598976..154602957,6	MCF-7	breast:
3	chr1:154523967..154525511-chr1:154600222..154602147,2	MCF-7	breast:
4	chr1:154579004..154583932-chr1:154594616..154602031,16	K562	blood:
5	chr1:154573864..154581870-chr1:154594652..154602962,18	K562	blood:
6	chr1:154574387..154584697-chr1:154596875..154603021,22	MCF-7	breast:
7	chr1:154575429..154582917-chr1:154596773..154602552,13	MCF-7	breast:
8	chr1:154529257..154532572-chr1:154598516..154601356,4	MCF-7	breast:
9	chr1:154538647..154541547-chr1:154599506..154601498,3	K562	blood:
10	chr1:154583710..154591836-chr1:154598416..154602140,15	MCF-7	breast:

Variant related genes	Relation type
ADAR	TF binding region
ENSG00000160714	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000160716	Chromatin interaction
ENSG00000268141	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11264221	0.81[AFR][1000 genomes]
rs11264231	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11264232	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12079381	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12086987	0.96[YRI][hapmap];0.91[AFR][1000 genomes]
rs12092890	0.81[AFR][1000 genomes]
rs12094866	0.90[AFR][1000 genomes]
rs1542796	0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs2172708	0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs6677920	0.87[YRI][hapmap];0.85[AFR][1000 genomes]
rs6683149	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs6690277	0.87[YRI][hapmap];0.81[AFR][1000 genomes]
rs7513474	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427095	0.81[YRI][hapmap];0.86[AFR][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	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
2	nsv521887	chr1:154236570-154684106	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
4	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv470740	chr1:154568683-154796895	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv464050	chr1:154568683-154801247	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
7	nsv547958	chr1:154568683-154801247	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154599000-154600800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:154599000-154601000	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr1:154599000-154601000	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr1:154599200-154600800	Active TSS	H9 Cell Line	embryonic stem cell
5	chr1:154599200-154600800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr1:154599200-154600800	Active TSS	Fetal Intestine Large	intestine
7	chr1:154599200-154600800	Active TSS	NHLF	lung
8	chr1:154599200-154601000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
9	chr1:154599200-154601000	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:154599400-154600800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr1:154599400-154600800	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:154599400-154600800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr1:154599400-154600800	Active TSS	iPS-15b Cell Line	embryonic stem cell
14	chr1:154599400-154600800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:154599400-154600800	Active TSS	Primary T helper cells PMA-I stimulated	--
16	chr1:154599400-154600800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:154599400-154600800	Active TSS	Ovary	ovary
18	chr1:154599400-154601000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:154599400-154601000	Active TSS	HUES64 Cell Line	embryonic stem cell
20	chr1:154599400-154601000	Active TSS	Pancreatic Islets	Pancreatic Islet
21	chr1:154599600-154600800	Active TSS	H1 Cell Line	embryonic stem cell
22	chr1:154599600-154600800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:154599600-154600800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr1:154599600-154600800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr1:154599600-154600800	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:154599600-154600800	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr1:154599600-154600800	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr1:154599600-154600800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr1:154599600-154600800	Active TSS	Aorta	Aorta
30	chr1:154599600-154600800	Active TSS	Brain Cingulate Gyrus	brain
31	chr1:154599600-154600800	Active TSS	Colonic Mucosa	Colon
32	chr1:154599600-154600800	Active TSS	Duodenum Smooth Muscle	Duodenum
33	chr1:154599600-154600800	Active TSS	Fetal Brain Female	brain
34	chr1:154599600-154600800	Active TSS	Fetal Intestine Small	intestine
35	chr1:154599600-154600800	Active TSS	Fetal Kidney	kidney
36	chr1:154599600-154600800	Active TSS	Pancreas	Pancrea
37	chr1:154599600-154600800	Active TSS	Placenta Amnion	Placenta Amnion
38	chr1:154599600-154600800	Active TSS	Psoas Muscle	Psoas
39	chr1:154599600-154600800	Active TSS	Right Ventricle	heart
40	chr1:154599600-154600800	Active TSS	HSMM	muscle
41	chr1:154599600-154600800	Active TSS	HSMMtube	muscle
42	chr1:154599600-154600800	Active TSS	K562	blood
43	chr1:154599600-154601000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr1:154599600-154601000	Active TSS	HUES6 Cell Line	embryonic stem cell
45	chr1:154599600-154601000	Active TSS	Brain Angular Gyrus	brain
46	chr1:154599600-154601000	Active TSS	Brain Anterior Caudate	brain
47	chr1:154599600-154601000	Active TSS	Brain Inferior Temporal Lobe	brain
48	chr1:154599600-154601000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr1:154599600-154601000	Active TSS	Brain Substantia Nigra	brain
50	chr1:154599600-154601000	Active TSS	Fetal Lung	lung

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