Variant report

Variant	rs1749412
Chromosome Location	chr1:155829360-155829361
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	BHLHE40	chr1:155828858-155830514	GM12878	blood:	n/a	n/a
2	MAZ	chr1:155828948-155829451	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:155829265-155829513	SK-N-SH	brain:	n/a	n/a
4	CEBPB	chr1:155829050-155829791	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:155829333-155829382	H1-hESC	embryonic stem cell:	n/a	n/a
6	ELF1	chr1:155828935-155829482	K562	blood:	n/a	chr1:155829213-155829226
7	TBP	chr1:155829316-155829490	H1-hESC	embryonic stem cell:	n/a	n/a
8	NR2F2	chr1:155828677-155829542	K562	blood:	n/a	n/a
9	STAT3	chr1:155828863-155829360	MCF10A-Er-Src	breast:	n/a	n/a
10	TAF1	chr1:155828935-155829465	SK-N-SH	brain:	n/a	n/a
11	ELK4	chr1:155828954-155829418	Hela-S3	cervix:	n/a	n/a
12	ELK1	chr1:155829055-155829448	Hela-S3	cervix:	n/a	n/a
13	JUN	chr1:155828448-155831227	K562	blood:	n/a	chr1:155830459-155830472 chr1:155829792-155829803
14	REST	chr1:155828738-155831562	H1-neurons	neurons:	n/a	chr1:155830066-155830079 chr1:155829006-155829020 chr1:155830399-155830412
15	ELF1	chr1:155828947-155829494	SK-N-SH	brain:	n/a	chr1:155829213-155829226
16	SPI1	chr1:155829029-155829378	GM12891	blood:	n/a	n/a
17	YY1	chr1:155829147-155830582	H1-hESC	embryonic stem cell:	n/a	chr1:155830029-155830037 chr1:155830078-155830092 chr1:155829651-155829662 chr1:155830030-155830040 chr1:155830078-155830087 chr1:155830018-155830040 chr1:155830378-155830387
18	STAT5A	chr1:155828806-155830621	GM12878	blood:	n/a	chr1:155829998-155830010 chr1:155829965-155829977 chr1:155829969-155829981
19	POLR2A	chr1:155828760-155830864	U87	brain:	n/a	n/a
20	IRF1	chr1:155828956-155829519	K562	blood:	n/a	chr1:155828977-155828994 chr1:155829102-155829113 chr1:155829045-155829057 chr1:155829046-155829056
21	CTCF	chr1:155829340-155829490	GM12875	blood:	n/a	n/a
22	POLR2A	chr1:155829078-155831211	H1-hESC	embryonic stem cell:	n/a	n/a
23	ZKSCAN1	chr1:155828954-155829410	Hela-S3	cervix:	n/a	n/a
24	MAZ	chr1:155828769-155830972	IMR90	lung:	n/a	n/a
25	ELF1	chr1:155828951-155829460	HepG2	liver:	n/a	chr1:155829213-155829226
26	ELF1	chr1:155828744-155829604	HCT-116	colon:	n/a	chr1:155829213-155829226
27	GABPA	chr1:155829072-155829370	HepG2	liver:	n/a	n/a
28	MTA3	chr1:155829182-155830918	GM12878	blood:	n/a	n/a
29	ATF2	chr1:155828867-155829402	GM12878	blood:	n/a	n/a
30	POLR2A	chr1:155829054-155830756	GM12892	blood:	n/a	n/a
31	CTCF	chr1:155829300-155829450	GM12864	blood:	n/a	n/a
32	FOXM1	chr1:155828772-155829688	GM12878	blood:	n/a	n/a
33	RFX5	chr1:155829050-155829390	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr1:155829182-155829500	H1-hESC	embryonic stem cell:	n/a	n/a
35	TAF1	chr1:155829081-155830705	H1-neurons	neurons:	n/a	n/a
36	POLR2A	chr1:155828820-155830931	SK-N-SH	brain:	n/a	n/a
37	CTCF	chr1:155829260-155829410	GM12871	blood:	n/a	n/a
38	SIN3AK20	chr1:155828983-155829660	MCF-7	breast:	n/a	n/a
39	CTBP2	chr1:155829215-155829706	H1-hESC	embryonic stem cell:	n/a	n/a
40	GTF2F1	chr1:155829323-155829364	H1-hESC	embryonic stem cell:	n/a	n/a
41	POLR2A	chr1:155828979-155830613	GM18951	blood:	n/a	n/a
42	MYBL2	chr1:155828904-155829396	HepG2	liver:	n/a	n/a
43	ELK1	chr1:155829025-155829486	GM12878	blood:	n/a	n/a
44	HDAC2	chr1:155829068-155829603	MCF-7	breast:	n/a	n/a
45	ZEB1	chr1:155829072-155830153	GM12878	blood:	n/a	n/a
46	REST	chr1:155829047-155830622	H1-neurons	neurons:	n/a	chr1:155830066-155830079 chr1:155830399-155830412
47	GABPA	chr1:155828912-155829556	SK-N-SH	brain:	n/a	n/a
48	ELF1	chr1:155828963-155830531	GM12878	blood:	n/a	chr1:155830080-155830092 chr1:155829213-155829226
49	POLR2A	chr1:155828817-155829379	PFSK-1	brain:	n/a	n/a
50	SP1	chr1:155828862-155829441	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:155828536..155830676-chr1:155863027..155864768,2	MCF-7	breast:
2	chr1:155824896..155829386-chr1:155902844..155905236,4	MCF-7	breast:
3	chr1:155827720..155829517-chr1:156180623..156183701,3	K562	blood:
4	chr1:155825368..155829605-chr1:155879516..155883021,7	K562	blood:
5	chr1:155825171..155830547-chr1:155878470..155884979,12	K562	blood:
6	chr1:155827023..155830284-chr1:156022724..156025393,4	K562	blood:
7	chr1:155713796..155716545-chr1:155826802..155829458,2	K562	blood:

Variant related genes	Relation type
GON4L	TF binding region
ENSG00000132680	Chromatin interaction
ENSG00000201614	Chromatin interaction
ENSG00000260238	Chromatin interaction
ENSG00000203761	Chromatin interaction
ENSG00000143622	Chromatin interaction
ENSG00000116586	Chromatin interaction
ENSG00000160803	Chromatin interaction
ENSG00000160783	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs10796952	0.89[AMR][1000 genomes]
rs11264417	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes]
rs1621690	0.82[AFR][1000 genomes]
rs1625821	1.00[AMR][1000 genomes]
rs1627630	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs168343	1.00[AMR][1000 genomes]
rs171168	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes]
rs1749413	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749414	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749420	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1749422	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1756242	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1765280	0.97[AFR][1000 genomes]
rs1765283	0.82[AFR][1000 genomes]
rs1765286	0.83[AFR][1000 genomes]
rs1886618	0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2136920	1.00[AMR][1000 genomes]
rs2175389	1.00[AMR][1000 genomes]
rs2363017	1.00[AMR][1000 genomes]
rs2481623	0.88[AFR][1000 genomes]
rs2485470	0.87[AFR][1000 genomes]
rs2485472	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2666828	0.89[AMR][1000 genomes]
rs2686264	0.89[AMR][1000 genomes]
rs2885676	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2988999	0.89[AMR][1000 genomes]
rs348184	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs348188	0.89[AMR][1000 genomes]
rs348189	0.89[AMR][1000 genomes]
rs348191	1.00[AMR][1000 genomes]
rs348193	0.89[AMR][1000 genomes]
rs348197	1.00[AMR][1000 genomes]
rs348199	1.00[AMR][1000 genomes]
rs348200	1.00[AMR][1000 genomes]
rs348207	0.96[YRI][hapmap];1.00[AMR][1000 genomes]
rs348208	1.00[AMR][1000 genomes]
rs348209	1.00[AMR][1000 genomes]
rs35264557	0.89[AMR][1000 genomes]
rs4581273	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs492669	0.89[AMR][1000 genomes]
rs4971058	0.89[AMR][1000 genomes]
rs512551	0.93[ASW][hapmap];0.82[MKK][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes]
rs540380	1.00[ASW][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes]
rs568672	1.00[AMR][1000 genomes]
rs606755	1.00[AMR][1000 genomes]
rs607036	0.81[ASW][hapmap];0.89[AMR][1000 genomes]
rs617232	0.81[ASW][hapmap];0.89[AMR][1000 genomes]
rs6427290	0.95[AFR][1000 genomes]
rs6688399	0.93[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs670787	0.89[AMR][1000 genomes]
rs708607	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs708609	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs708613	0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8179457	1.00[AMR][1000 genomes]
rs822013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822014	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822017	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822021	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822023	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822024	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822027	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822479	0.86[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822481	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822483	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822485	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822487	0.97[AFR][1000 genomes]
rs822492	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822496	1.00[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs822498	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs822521	0.93[ASW][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes]
rs822522	1.00[AMR][1000 genomes]
rs822524	0.81[AFR][1000 genomes]
rs866603	1.00[ASW][hapmap];0.94[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427219	0.89[AMR][1000 genomes]
rs9427222	1.00[AMR][1000 genomes]
rs9427227	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9427229	0.81[AFR][1000 genomes];1.00[AMR][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	esv33869	chr1:155223283-155917961	Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	esv3423892	chr1:155664084-155901487	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1003170	chr1:155762204-155836564	Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Enhancers Genic enhancers 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	14 gene(s)	inside rSNPs	diseases
4	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 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	chr1:155826400-155829600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr1:155826600-155829400	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr1:155827000-155829400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:155827000-155829400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:155827000-155829400	Weak transcription	Lung	lung
6	chr1:155827200-155829400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:155827200-155829400	Weak transcription	Gastric	stomach
8	chr1:155827200-155829600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:155827200-155829800	Flanking Active TSS	Dnd41	blood
10	chr1:155827400-155829400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr1:155828000-155829600	Active TSS	HepG2	liver
12	chr1:155828200-155829600	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr1:155828200-155830400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
14	chr1:155828400-155829400	Active TSS	Stomach Smooth Muscle	stomach
15	chr1:155828400-155829400	Active TSS	A549	lung
16	chr1:155828400-155829400	Active TSS	GM12878-XiMat	blood
17	chr1:155828400-155829400	Active TSS	HSMM	muscle
18	chr1:155828400-155829400	Active TSS	NHDF-Ad	bronchial
19	chr1:155828400-155829600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:155828400-155830600	Active TSS	Psoas Muscle	Psoas
21	chr1:155828400-155831000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr1:155828600-155829400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr1:155828600-155829400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:155828600-155829400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:155828600-155829400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr1:155828600-155829400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:155828600-155829400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:155828600-155829400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:155828600-155829400	Active TSS	Brain Germinal Matrix	brain
30	chr1:155828600-155829400	Active TSS	Duodenum Mucosa	Duodenum
31	chr1:155828600-155829400	Active TSS	Fetal Brain Female	brain
32	chr1:155828600-155829400	Active TSS	Right Ventricle	heart
33	chr1:155828600-155829400	Active TSS	HSMMtube	muscle
34	chr1:155828600-155829600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr1:155828600-155829600	Active TSS	Ovary	ovary
36	chr1:155828600-155829600	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr1:155828600-155830000	Active TSS	Thymus	Thymus
38	chr1:155828600-155830200	Flanking Active TSS	Primary hematopoietic stem cells	blood
39	chr1:155828600-155830600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr1:155828600-155830600	Active TSS	Brain Anterior Caudate	brain
41	chr1:155828600-155830600	Active TSS	Brain Hippocampus Middle	brain
42	chr1:155828600-155830600	Active TSS	Rectal Smooth Muscle	rectum
43	chr1:155828600-155830800	Active TSS	Brain Inferior Temporal Lobe	brain
44	chr1:155828600-155830800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr1:155828600-155830800	Active TSS	Fetal Kidney	kidney
46	chr1:155828600-155831000	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:155828800-155829400	Active TSS	H9 Cell Line	embryonic stem cell
48	chr1:155828800-155829400	Active TSS	Muscle Satellite Cultured Cells	--
49	chr1:155828800-155829400	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr1:155828800-155829400	Active TSS	Fetal Intestine Small	intestine

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