Variant report

Variant	rs1534984
Chromosome Location	chr1:169074736-169074737
allele	C/G
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	YY1	chr1:169074717-169076226	HepG2	liver:	n/a	chr1:169075170-169075184 chr1:169076011-169076025 chr1:169075340-169075351 chr1:169075310-169075321 chr1:169075317-169075331 chr1:169075343-169075352 chr1:169074975-169074989 chr1:169075943-169075954 chr1:169075346-169075355 chr1:169076186-169076197 chr1:169075466-169075480
2	RAD21	chr1:169074631-169075735	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr1:169074725-169075336	H1-hESC	embryonic stem cell:	n/a	n/a
4	USF1	chr1:169074641-169075007	A549	lung:	n/a	chr1:169074804-169074815 chr1:169074805-169074814 chr1:169074800-169074821
5	HDAC2	chr1:169074683-169075234	HepG2	liver:	n/a	n/a
6	TCF12	chr1:169074584-169075322	ECC-1	luminal epithelium:	n/a	chr1:169075044-169075054 chr1:169075253-169075260
7	RAD21	chr1:169074715-169075144	HepG2	liver:	n/a	n/a
8	MAX	chr1:169074604-169075874	HepG2	liver:	n/a	chr1:169075667-169075677 chr1:169075347-169075357
9	POLR2A	chr1:169074617-169076516	GM19193	blood:	n/a	n/a
10	MAX	chr1:169074556-169076383	H1-hESC	embryonic stem cell:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357
11	SIN3AK20	chr1:169074606-169077295	MCF-7	breast:	n/a	n/a
12	USF1	chr1:169074610-169075055	A549	lung:	n/a	chr1:169074804-169074815 chr1:169074805-169074814 chr1:169074800-169074821
13	HA-E2F1	chr1:169074633-169076791	MCF-7	breast:	n/a	chr1:169075469-169075479 chr1:169075349-169075358 chr1:169076005-169076019 chr1:169075065-169075074 chr1:169075344-169075354 chr1:169075044-169075054 chr1:169075666-169075675
14	E2F6	chr1:169074599-169075449	H1-hESC	embryonic stem cell:	n/a	chr1:169075349-169075358 chr1:169075065-169075074 chr1:169075344-169075354 chr1:169075044-169075054
15	CTCF	chr1:169074640-169074790	GM12870	blood:	n/a	n/a
16	EP300	chr1:169074558-169076305	ECC-1	luminal epithelium:	n/a	chr1:169075030-169075043 chr1:169075296-169075312 chr1:169076181-169076197 chr1:169076180-169076196 chr1:169076033-169076049 chr1:169075343-169075352
17	MAX	chr1:169074718-169075847	HepG2	liver:	n/a	chr1:169075667-169075677 chr1:169075347-169075357
18	MAX	chr1:169074502-169076839	A549	lung:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357
19	GATA3	chr1:169074637-169076056	MCF-7	breast:	n/a	chr1:169074711-169074722
20	CTCF	chr1:169074620-169074770	GM12875	blood:	n/a	n/a
21	CREB1	chr1:169074714-169076584	HepG2	liver:	n/a	n/a
22	POLR2A	chr1:169074709-169082197	HepG2	liver:	n/a	n/a
23	YY1	chr1:169074521-169075196	H1-hESC	embryonic stem cell:	n/a	chr1:169075170-169075184 chr1:169074975-169074989
24	ZBTB7A	chr1:169074709-169075996	ECC-1	luminal epithelium:	n/a	chr1:169075276-169075283 chr1:169075791-169075802 chr1:169075732-169075743
25	USF1	chr1:169074607-169075140	ECC-1	luminal epithelium:	n/a	chr1:169075043-169075059 chr1:169074804-169074815 chr1:169074805-169074814 chr1:169074800-169074821
26	BHLHE40	chr1:169074631-169075173	K562	blood:	n/a	chr1:169075043-169075059 chr1:169074805-169074814 chr1:169074800-169074821
27	MAX	chr1:169074630-169075264	H1-hESC	embryonic stem cell:	n/a	n/a
28	CTBP2	chr1:169074352-169076271	H1-hESC	embryonic stem cell:	n/a	n/a
29	MAX	chr1:169074518-169075766	H1-hESC	embryonic stem cell:	n/a	chr1:169075667-169075677 chr1:169075347-169075357
30	EP300	chr1:169074698-169076374	SK-N-SH	brain:	n/a	chr1:169075030-169075043 chr1:169075296-169075312 chr1:169076181-169076197 chr1:169076180-169076196 chr1:169076033-169076049 chr1:169075343-169075352
31	POLR2A	chr1:169074689-169076214	H1-hESC	embryonic stem cell:	n/a	n/a
32	MAZ	chr1:169074351-169076481	K562	blood:	n/a	chr1:169075667-169075677 chr1:169076272-169076282 chr1:169075347-169075357
33	E2F6	chr1:169074451-169075752	H1-hESC	embryonic stem cell:	n/a	chr1:169075469-169075479 chr1:169075615-169075626 chr1:169075349-169075358 chr1:169075065-169075074 chr1:169075344-169075354 chr1:169075044-169075054 chr1:169075666-169075675
34	USF1	chr1:169074572-169075213	ECC-1	luminal epithelium:	n/a	chr1:169075043-169075059 chr1:169074804-169074815 chr1:169074805-169074814 chr1:169074800-169074821
35	TCF12	chr1:169074677-169076330	ECC-1	luminal epithelium:	n/a	chr1:169075044-169075054 chr1:169075804-169075811 chr1:169075253-169075260
36	EGR1	chr1:169074697-169076363	HCT-116	colon:	n/a	chr1:169075344-169075357 chr1:169075345-169075354 chr1:169075341-169075355 chr1:169076271-169076281 chr1:169075344-169075357 chr1:169075037-169075052 chr1:169076262-169076272 chr1:169076275-169076285 chr1:169075348-169075358 chr1:169075344-169075357 chr1:169075038-169075051 chr1:169075041-169075051 chr1:169075344-169075354 chr1:169075344-169075357 chr1:169075666-169075676 chr1:169075034-169075056 chr1:169076272-169076285 chr1:169075038-169075051 chr1:169075065-169075075 chr1:169075339-169075361 chr1:169076275-169076284 chr1:169075039-169075053 chr1:169075345-169075356
37	MAX	chr1:169074518-169075926	A549	lung:	n/a	chr1:169075667-169075677 chr1:169075347-169075357
38	ZNF143	chr1:169074579-169075993	H1-hESC	embryonic stem cell:	n/a	chr1:169075549-169075559
39	TAF1	chr1:169074677-169075825	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr1:169074716-169076973	H1-neurons	neurons:	n/a	n/a
41	BHLHE40	chr1:169074635-169075218	GM12878	blood:	n/a	chr1:169074805-169074814 chr1:169074800-169074821 chr1:169075043-169075059
42	POLR2A	chr1:169074720-169075806	HepG2	liver:	n/a	n/a
43	EBF1	chr1:169074591-169075089	GM12878	blood:	n/a	n/a
44	MYBL2	chr1:169074699-169075306	HepG2	liver:	n/a	n/a
45	POLR2A	chr1:169074719-169076459	A549	lung:	n/a	n/a
46	MAX	chr1:169074678-169075570	A549	lung:	n/a	chr1:169075347-169075357
47	POLR2A	chr1:169074616-169076522	NB4	blood:	n/a	n/a
48	HEY1	chr1:169074632-169075762	HepG2	liver:	n/a	chr1:169075342-169075357 chr1:169075307-169075322 chr1:169075309-169075324 chr1:169075667-169075682
49	USF1	chr1:169074627-169075001	SK-N-SH_RA	brain:	n/a	chr1:169074804-169074815 chr1:169074805-169074814 chr1:169074800-169074821
50	USF1	chr1:169074605-169075030	A549	lung:	n/a	chr1:169074804-169074815 chr1:169074805-169074814 chr1:169074800-169074821

No.	Distal block	Cell Line	Cell type
1	chr1:169055830..169060702-chr1:169073415..169077056,5	MCF-7	breast:
2	chr1:169073561..169077593-chr1:169336088..169341683,7	K562	blood:
3	chr1:169073666..169076222-chr8:146016630..146018644,2	MCF-7	breast:
4	chr1:169073988..169075864-chr6:26199270..26200811,2	MCF-7	breast:
5	chr1:169073990..169076920-chr1:169277266..169279793,2	K562	blood:
6	chr1:169053133..169065213-chr1:169070028..169077898,15	MCF-7	breast:

Variant related genes	Relation type
ATP1B1	TF binding region
ENSG00000197846	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000117475	Chromatin interaction
ENSG00000161016	Chromatin interaction
ENSG00000143156	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000203601	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12061601	0.91[EUR][1000 genomes]
rs12079856	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12751593	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1320976	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1320977	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1892092	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1892093	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28362572	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28362573	0.93[ASN][1000 genomes]
rs4656647	0.88[EUR][1000 genomes]
rs59732929	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672876	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
6	esv3323390	chr1:169074353-169076901	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169072200-169074800	Weak transcription	Right Atrium	heart
2	chr1:169072400-169075000	Weak transcription	Aorta	Aorta
3	chr1:169072600-169074800	Enhancers	Brain Substantia Nigra	brain
4	chr1:169072800-169074800	Enhancers	Esophagus	oesophagus
5	chr1:169073200-169074800	Weak transcription	Ovary	ovary
6	chr1:169073200-169074800	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr1:169073200-169075000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
8	chr1:169073400-169074800	Enhancers	Small Intestine	intestine
9	chr1:169074000-169075000	Enhancers	Fetal Brain Male	brain
10	chr1:169074000-169078800	Active TSS	Rectal Smooth Muscle	rectum
11	chr1:169074200-169074800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr1:169074200-169074800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:169074200-169074800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr1:169074200-169074800	Enhancers	Lung	lung
15	chr1:169074200-169074800	Enhancers	Spleen	Spleen
16	chr1:169074200-169075000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr1:169074200-169075000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
18	chr1:169074400-169074800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
19	chr1:169074400-169074800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
20	chr1:169074400-169074800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:169074400-169074800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:169074400-169074800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:169074400-169074800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr1:169074400-169074800	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:169074400-169074800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:169074400-169074800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
27	chr1:169074400-169074800	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr1:169074400-169074800	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr1:169074400-169074800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:169074400-169074800	Bivalent Enhancer	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:169074400-169074800	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr1:169074400-169074800	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:169074400-169074800	Flanking Active TSS	Brain Germinal Matrix	brain
34	chr1:169074400-169074800	Flanking Active TSS	Brain Hippocampus Middle	brain
35	chr1:169074400-169074800	Flanking Active TSS	Fetal Kidney	kidney
36	chr1:169074400-169074800	Enhancers	Fetal Lung	lung
37	chr1:169074400-169074800	Bivalent Enhancer	Placenta	Placenta
38	chr1:169074400-169074800	Bivalent Enhancer	Fetal Thymus	thymus
39	chr1:169074400-169074800	Enhancers	Placenta Amnion	Placenta Amnion
40	chr1:169074400-169074800	Flanking Active TSS	Stomach Mucosa	stomach
41	chr1:169074400-169074800	Flanking Active TSS	A549	lung
42	chr1:169074400-169074800	Bivalent Enhancer	K562	blood
43	chr1:169074400-169075000	Flanking Active TSS	Liver	Liver
44	chr1:169074400-169075000	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr1:169074400-169075000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr1:169074400-169075000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr1:169074400-169075000	Flanking Active TSS	Hela-S3	cervix
48	chr1:169074400-169075000	Flanking Active TSS	HepG2	liver
49	chr1:169074400-169075200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr1:169074400-169075200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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