Variant report

Variant	rs822729
Chromosome Location	chr1:228296843-228296844
allele	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	POLR2A	chr1:228296659-228297799	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr1:228296756-228297410	GM12891	blood:	n/a	n/a
3	POLR2A	chr1:228296622-228298090	GM12878	blood:	n/a	n/a
4	SP1	chr1:228296744-228297430	GM12878	blood:	n/a	chr1:228297140-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297120-228297129 chr1:228297119-228297131 chr1:228297087-228297097 chr1:228297140-228297149 chr1:228297141-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297088-228297097 chr1:228297119-228297131 chr1:228297140-228297150 chr1:228297121-228297130
5	SMC3	chr1:228296805-228297209	Hela-S3	cervix:	n/a	n/a
6	SRF	chr1:228296778-228297268	H1-hESC	embryonic stem cell:	n/a	chr1:228297184-228297194 chr1:228297091-228297101 chr1:228297140-228297150
7	MAFK	chr1:228296835-228297225	Hela-S3	cervix:	n/a	n/a
8	TEAD4	chr1:228296759-228297225	H1-hESC	embryonic stem cell:	n/a	n/a
9	MXI1	chr1:228296798-228297153	H1-hESC	embryonic stem cell:	n/a	n/a
10	POLR2A	chr1:228296748-228297410	HepG2	liver:	n/a	n/a
11	CCNT2	chr1:228296776-228297394	K562	blood:	n/a	n/a
12	PML	chr1:228296796-228297311	GM12878	blood:	n/a	n/a
13	POLR2A	chr1:228296762-228297332	SK-N-SH	brain:	n/a	n/a
14	TCF12	chr1:228296692-228297526	ECC-1	luminal epithelium:	n/a	n/a
15	POLR2A	chr1:228296723-228297445	GM18526	blood:	n/a	n/a
16	TAF1	chr1:228296725-228297393	PFSK-1	brain:	n/a	n/a
17	POLR2A	chr1:228296645-228297332	HUVEC	blood vessel:	n/a	n/a
18	ATF3	chr1:228296810-228297244	H1-hESC	embryonic stem cell:	n/a	chr1:228297098-228297107
19	POLR2A	chr1:228296726-228297338	A549	lung:	n/a	n/a
20	BRCA1	chr1:228296811-228297237	Hela-S3	cervix:	n/a	n/a
21	FOSL2	chr1:228296785-228297382	HepG2	liver:	n/a	n/a
22	SRF	chr1:228296642-228297331	ECC-1	luminal epithelium:	n/a	chr1:228297184-228297194 chr1:228297091-228297101 chr1:228297140-228297150
23	MYC	chr1:228296803-228297195	MCF-7	breast:	n/a	chr1:228297140-228297150
24	YY1	chr1:228296757-228297392	GM12878	blood:	n/a	chr1:228297226-228297240 chr1:228297180-228297194 chr1:228297186-228297197
25	TCF7L2	chr1:228296821-228297136	PANC-1	pancreas:	n/a	n/a
26	USF1	chr1:228296841-228297387	H1-hESC	embryonic stem cell:	n/a	n/a
27	SRF	chr1:228296793-228297243	K562	blood:	n/a	chr1:228297184-228297194 chr1:228297091-228297101 chr1:228297140-228297150
28	CEBPB	chr1:228296819-228297367	HepG2	liver:	n/a	n/a
29	POLR2A	chr1:228296432-228297439	K562	blood:	n/a	n/a
30	POLR2A	chr1:228296741-228297434	K562	blood:	n/a	n/a
31	JUND	chr1:228296842-228297186	HepG2	liver:	n/a	n/a
32	POLR2A	chr1:228296531-228297510	ECC-1	luminal epithelium:	n/a	n/a
33	JUND	chr1:228296728-228297347	A549	lung:	n/a	n/a
34	POLR2A	chr1:228296631-228297505	MCF-7	breast:	n/a	n/a
35	SP1	chr1:228296387-228297568	HCT-116	colon:	n/a	chr1:228297140-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297120-228297129 chr1:228297119-228297131 chr1:228297087-228297097 chr1:228297140-228297149 chr1:228297141-228297150 chr1:228297139-228297151 chr1:228297086-228297098 chr1:228297088-228297097 chr1:228297119-228297131 chr1:228297140-228297150 chr1:228297121-228297130
36	POLR2A	chr1:228296611-228297758	GM19193	blood:	n/a	n/a
37	E2F4	chr1:228296586-228297268	K562	blood:	n/a	chr1:228297144-228297154 chr1:228297184-228297194 chr1:228297096-228297105 chr1:228297120-228297132 chr1:228297091-228297101
38	GATA2	chr1:228296806-228297579	SH-SY5Y	brain:	n/a	n/a
39	NFATC1	chr1:228296779-228297197	GM12878	blood:	n/a	n/a
40	MTA3	chr1:228296665-228297065	GM12878	blood:	n/a	n/a
41	EGR1	chr1:228296769-228297451	MCF-7	breast:	n/a	chr1:228297139-228297149 chr1:228297055-228297062 chr1:228297150-228297163 chr1:228297140-228297150 chr1:228297049-228297062
42	POLR2A	chr1:228296721-228297595	GM15510	blood:	n/a	n/a
43	MYC	chr1:228296766-228297428	K562	blood:	n/a	chr1:228297140-228297150
44	TAF1	chr1:228296703-228297487	H1-neurons	neurons:	n/a	n/a
45	RFX5	chr1:228296793-228297330	HepG2	liver:	n/a	n/a
46	SP2	chr1:228296782-228297212	K562	blood:	n/a	n/a
47	ETS1	chr1:228296744-228297439	K562	blood:	n/a	n/a
48	CEBPD	chr1:228296723-228297449	HepG2	liver:	n/a	n/a
49	EBF1	chr1:228295768-228297810	GM12878	blood:	n/a	chr1:228296439-228296450
50	HMGN3	chr1:228296752-228297717	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:228295623..228298108-chr1:228335544..228338438,2	MCF-7	breast:
2	chr1:228294222..228297212-chr1:228327852..228330069,2	MCF-7	breast:
3	chr1:228295318..228298683-chr1:228360322..228363984,4	K562	blood:
4	chr1:228295479..228298124-chr1:228352385..228354527,2	MCF-7	breast:
5	chr1:228296750..228297459-chr10:71930025..71930697,2	NB4	blood:
6	chr1:228266682..228273620-chr1:228293839..228298603,9	MCF-7	breast:
7	chr1:228296521..228297220-chr3:150321016..150321544,2	NB4	blood:
8	chr1:228292983..228294840-chr1:228295520..228297774,2	MCF-7	breast:
9	chr1:228274118..228278669-chr1:228294195..228297645,6	MCF-7	breast:
10	chr1:228296521..228297564-chr1:228327615..228328500,3	Hela-S3	cervix:
11	chr1:228293945..228298846-chr1:228325398..228330582,13	K562	blood:
12	chr1:228294705..228298588-chr1:228325821..228329680,6	MCF-7	breast:
13	chr1:228295591..228297111-chr1:228358549..228360057,2	K562	blood:
14	chr1:228296537..228297467-chr15:75493986..75494523,2	Hela-S3	cervix:
15	chr1:228296738..228297414-chr7:44836178..44836722,2	NB4	blood:
16	chr1:228295286..228298610-chr1:228351640..228355026,4	K562	blood:
17	chr1:228294689..228298417-chr1:228352364..228354856,6	MCF-7	breast:
18	chr1:228295402..228297803-chr1:228330568..228332279,2	MCF-7	breast:
19	chr1:228288384..228298705-chr1:228351640..228357240,26	K562	blood:
20	chr1:228295585..228298584-chr1:228645620..228647778,2	K562	blood:
21	chr1:228293945..228298682-chr1:228326047..228331152,9	K562	blood:
22	chr1:228270227..228270808-chr1:228296563..228297459,2	NB4	blood:
23	chr1:228295585..228298429-chr1:228645232..228648455,3	K562	blood:
24	chr1:228295500..228297827-chr1:228593936..228595478,2	K562	blood:

Variant related genes	Relation type
C1orf35	TF binding region
MRPL55	TF binding region
ENSG00000231563	Chromatin interaction
ENSG00000181218	Chromatin interaction
ENSG00000203684	Chromatin interaction
ENSG00000198835	Chromatin interaction
ENSG00000167173	Chromatin interaction
ENSG00000196262	Chromatin interaction
ENSG00000181873	Chromatin interaction
ENSG00000154370	Chromatin interaction
ENSG00000143774	Chromatin interaction
ENSG00000196890	Chromatin interaction
ENSG00000143761	Chromatin interaction
ENSG00000079332	Chromatin interaction
ENSG00000198843	Chromatin interaction
ENSG00000143793	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10916269	0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs1094601	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1188976	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs1771454	0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs1771466	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs1771475	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1856871	0.87[AFR][1000 genomes]
rs1934882	0.82[YRI][hapmap]
rs4653534	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6686210	0.86[YRI][hapmap]
rs6698730	0.95[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs73092925	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7534419	1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs822728	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822731	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822732	0.81[YRI][hapmap];0.82[AFR][1000 genomes]
rs822735	0.83[AMR][1000 genomes]
rs822737	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs822741	0.81[YRI][hapmap]
rs822742	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs849750	0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs947086	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010605	chr1:227770415-228332690	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
3	nsv427952	chr1:227881664-228308629	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
5	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
6	nsv832803	chr1:228155118-228313681	Transcr. at gene 5' and 3' Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv873252	chr1:228174528-228371551	Strong transcription Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
8	nsv873253	chr1:228231601-228537942	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
9	nsv873254	chr1:228231601-228543800	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
10	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	133 gene(s)	inside rSNPs	diseases
11	nsv482143	chr1:228294380-228297013	Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228295800-228297000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:228295800-228297000	Flanking Active TSS	Stomach Smooth Muscle	stomach
3	chr1:228295800-228297400	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:228295800-228297800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:228296000-228297400	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr1:228296000-228297600	Active TSS	iPS-20b Cell Line	embryonic stem cell
7	chr1:228296000-228297600	Active TSS	A549	lung
8	chr1:228296000-228298000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:228296000-228298000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
10	chr1:228296000-228298200	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr1:228296200-228297000	Flanking Active TSS	Primary B cells from cord blood	blood
12	chr1:228296200-228297000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:228296200-228297000	Flanking Active TSS	Colonic Mucosa	Colon
14	chr1:228296200-228297000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr1:228296200-228297400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:228296200-228297600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:228296200-228297600	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
18	chr1:228296200-228297800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
19	chr1:228296200-228297800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:228296200-228297800	Bivalent/Poised TSS	HepG2	liver
21	chr1:228296200-228298000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:228296200-228298200	Active TSS	ES-I3 Cell Line	embryonic stem cell
23	chr1:228296400-228297400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr1:228296400-228297600	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr1:228296400-228297600	Active TSS	iPS-15b Cell Line	embryonic stem cell
26	chr1:228296400-228297600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
27	chr1:228296400-228297600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr1:228296400-228297600	Active TSS	Hela-S3	cervix
29	chr1:228296400-228297600	Active TSS	HSMM	muscle
30	chr1:228296400-228297600	Active TSS	K562	blood
31	chr1:228296400-228297600	Active TSS	NHEK	skin
32	chr1:228296400-228297800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr1:228296400-228297800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr1:228296400-228297800	Active TSS	HUES48 Cell Line	embryonic stem cell
35	chr1:228296400-228297800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:228296400-228297800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:228296400-228297800	Active TSS	Fetal Intestine Large	intestine
38	chr1:228296400-228297800	Active TSS	Gastric	stomach
39	chr1:228296400-228297800	Active TSS	Left Ventricle	heart
40	chr1:228296400-228298000	Active TSS	H9 Cell Line	embryonic stem cell
41	chr1:228296400-228298000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:228296400-228298000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr1:228296400-228298000	Active TSS	Aorta	Aorta
44	chr1:228296400-228298000	Active TSS	Ovary	ovary
45	chr1:228296400-228298000	Active TSS	Psoas Muscle	Psoas
46	chr1:228296400-228298000	Active TSS	GM12878-XiMat	blood
47	chr1:228296400-228298000	Active TSS	HMEC	breast
48	chr1:228296400-228298000	Active TSS	NHDF-Ad	bronchial
49	chr1:228296400-228298200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr1:228296600-228297000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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