Variant report

Variant	rs74116267
Chromosome Location	chr1:154948698-154948699
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	POLR2A	chr1:154945991-154949108	K562	blood:	n/a	n/a
2	POLR2A	chr1:154948426-154948804	H1-hESC	embryonic stem cell:	n/a	n/a
3	CEBPB	chr1:154946020-154948730	Hela-S3	cervix:	n/a	chr1:154947053-154947061
4	POLR2A	chr1:154948684-154948703	MCF-7	breast:	n/a	n/a
5	POLR2A	chr1:154945898-154948805	K562	blood:	n/a	n/a
6	POLR2A	chr1:154944760-154948847	HepG2	liver:	n/a	n/a
7	POLR2A	chr1:154946042-154948839	GM12891	blood:	n/a	n/a
8	MYC	chr1:154948432-154948728	MCF10A-Er-Src	breast:	n/a	n/a
9	POLR2A	chr1:154945872-154949046	HCT-116	colon:	n/a	n/a
10	POLR2A	chr1:154948597-154948880	HepG2	liver:	n/a	n/a
11	SIN3A	chr1:154946119-154948958	GM12878	blood:	n/a	n/a
12	GTF2F1	chr1:154945953-154948738	Hela-S3	cervix:	n/a	n/a
13	WRNIP1	chr1:154948420-154949220	GM12878	blood:	n/a	n/a
14	CHD1	chr1:154944665-154949367	IMR90	lung:	n/a	n/a
15	TBP	chr1:154944835-154949268	Hela-S3	cervix:	n/a	n/a
16	POLR2A	chr1:154944641-154948874	PANC-1	pancreas:	n/a	n/a
17	JUN	chr1:154945878-154949491	K562	blood:	n/a	chr1:154946685-154946696 chr1:154946687-154946699 chr1:154946688-154946698 chr1:154948175-154948184 chr1:154946689-154946698 chr1:154946688-154946698 chr1:154946688-154946698 chr1:154946718-154946726 chr1:154947054-154947063 chr1:154946964-154946973 chr1:154946688-154946698
18	POLR2A	chr1:154946081-154948827	GM12878	blood:	n/a	n/a
19	MXI1	chr1:154946011-154948985	Hela-S3	cervix:	n/a	n/a
20	MYC	chr1:154946015-154948765	K562	blood:	n/a	n/a
21	MXI1	chr1:154946033-154948741	GM12878	blood:	n/a	n/a
22	MXI1	chr1:154945906-154949299	SK-N-SH	brain:	n/a	n/a
23	MAFK	chr1:154948371-154948987	Hela-S3	cervix:	n/a	n/a
24	EP300	chr1:154948294-154948815	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:154945940-154948751	K562	blood:	n/a	n/a
26	POLR2A	chr1:154946040-154948838	GM12878	blood:	n/a	n/a
27	CHD1	chr1:154947139-154948919	GM12878	blood:	n/a	n/a
28	MTA3	chr1:154948064-154948917	GM12878	blood:	n/a	n/a
29	HEY1	chr1:154945998-154948760	K562	blood:	n/a	n/a
30	POLR2A	chr1:154944774-154948815	MCF10A-Er-Src	breast:	n/a	n/a
31	MYC	chr1:154946027-154948778	K562	blood:	n/a	n/a
32	POLR2A	chr1:154946196-154948834	GM12878	blood:	n/a	n/a
33	RELA	chr1:154946237-154948871	GM15510	blood:	n/a	n/a
34	SIN3A	chr1:154945975-154948826	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:154944642-154948742	PANC-1	pancreas:	n/a	n/a
36	MTA3	chr1:154945944-154948762	GM12878	blood:	n/a	n/a
37	POLR2A	chr1:154945862-154948819	PFSK-1	brain:	n/a	n/a
38	TBP	chr1:154946070-154948709	GM12878	blood:	n/a	n/a
39	HCFC1	chr1:154944622-154948767	Hela-S3	cervix:	n/a	n/a
40	MAX	chr1:154945982-154948840	A549	lung:	n/a	n/a
41	TBL1XR1	chr1:154946096-154948709	GM12878	blood:	n/a	n/a
42	POLR2A	chr1:154942306-154949253	H1-hESC	embryonic stem cell:	n/a	n/a
43	IRF1	chr1:154946006-154949322	K562	blood:	n/a	chr1:154948298-154948311 chr1:154948296-154948310 chr1:154946328-154946342 chr1:154949031-154949045 chr1:154948301-154948312 chr1:154948294-154948315 chr1:154946232-154946246 chr1:154946312-154946326 chr1:154946623-154946637 chr1:154946014-154946034 chr1:154948300-154948311 chr1:154946021-154946034 chr1:154948298-154948311 chr1:154948302-154948312 chr1:154946923-154946932 chr1:154948298-154948312 chr1:154948299-154948312 chr1:154948299-154948313 chr1:154948299-154948313 chr1:154948298-154948311 chr1:154947352-154947361 chr1:154946132-154946142 chr1:154948297-154948311
44	POLR2A	chr1:154945953-154948911	PFSK-1	brain:	n/a	n/a
45	MXI1	chr1:154945880-154949112	IMR90	lung:	n/a	n/a
46	CHD1	chr1:154948299-154948756	H1-hESC	embryonic stem cell:	n/a	n/a
47	POLR2A	chr1:154944584-154948761	SK-N-SH	brain:	n/a	n/a
48	TEAD4	chr1:154945927-154948831	K562	blood:	n/a	n/a
49	GATA3	chr1:154948495-154948861	T-47D	breast:	n/a	n/a
50	TBL1XR1	chr1:154948373-154948786	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154943492..154949367-chr1:155033837..155038035,9	MCF-7	breast:
2	chr1:154573844..154576580-chr1:154947411..154949636,2	K562	blood:
3	chr1:154948216..154948719-chr12:104323817..104324703,2	Hela-S3	cervix:
4	chr1:154948517..154951842-chr1:155034906..155036770,3	MCF-7	breast:
5	chr1:154947156..154950628-chr1:155023259..155025337,3	MCF-7	breast:
6	chr1:154943580..154949331-chr1:155014649..155018913,6	MCF-7	breast:
7	chr1:11968639..11970236-chr1:154947682..154949521,2	K562	blood:
8	chr1:154944682..154948805-chr1:155021065..155026491,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHC1-1	chr1:154948628-154948763	NONHSAT006659

Variant related genes	Relation type
CKS1B	TF binding region
SHC1	TF binding region
ENSG00000214198	Chromatin interaction
ENSG00000232093	Chromatin interaction
ENSG00000201801	Chromatin interaction
ENSG00000265072	Chromatin interaction
ENSG00000160710	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000166598	Chromatin interaction
ENSG00000143537	Chromatin interaction
ENSG00000243364	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1395561	1.00[AMR][1000 genomes]
rs16836381	1.00[AMR][1000 genomes]
rs55699206	1.00[AMR][1000 genomes]
rs57393028	1.00[AMR][1000 genomes]
rs6657775	1.00[AMR][1000 genomes]
rs6681539	1.00[AMR][1000 genomes]
rs6682049	1.00[AMR][1000 genomes]
rs6699247	1.00[AMR][1000 genomes]
rs73005493	1.00[AMR][1000 genomes]
rs73005497	1.00[AMR][1000 genomes]
rs73007703	1.00[AMR][1000 genomes]
rs74115892	1.00[AMR][1000 genomes]
rs74116261	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
3	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154941000-154949000	Active TSS	H9 Cell Line	embryonic stem cell
2	chr1:154944200-154948800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:154944600-154948800	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:154945000-154949200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr1:154945400-154948800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:154945600-154948800	Active TSS	A549	lung
7	chr1:154945600-154949000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr1:154945600-154949000	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr1:154945800-154948800	Active TSS	HUES48 Cell Line	embryonic stem cell
10	chr1:154945800-154948800	Active TSS	HUES6 Cell Line	embryonic stem cell
11	chr1:154945800-154948800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:154945800-154948800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
13	chr1:154945800-154948800	Active TSS	Esophagus	oesophagus
14	chr1:154945800-154948800	Active TSS	Fetal Intestine Large	intestine
15	chr1:154945800-154948800	Active TSS	Stomach Mucosa	stomach
16	chr1:154945800-154948800	Active TSS	GM12878-XiMat	blood
17	chr1:154945800-154948800	Active TSS	NHDF-Ad	bronchial
18	chr1:154945800-154949000	Active TSS	iPS-20b Cell Line	embryonic stem cell
19	chr1:154945800-154949200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr1:154945800-154949200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:154945800-154949400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:154945800-154949600	Active TSS	H1 Cell Line	embryonic stem cell
23	chr1:154946000-154948800	Active TSS	Fetal Intestine Small	intestine
24	chr1:154946000-154948800	Active TSS	Ovary	ovary
25	chr1:154946000-154948800	Active TSS	Placenta Amnion	Placenta Amnion
26	chr1:154946000-154948800	Active TSS	NHLF	lung
27	chr1:154946200-154948800	Active TSS	Lung	lung
28	chr1:154946200-154948800	Active TSS	HSMMtube	muscle
29	chr1:154946200-154949000	Active TSS	HSMM	muscle
30	chr1:154946200-154949000	Active TSS	NHEK	skin
31	chr1:154946400-154948800	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:154947200-154949000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
33	chr1:154947400-154948800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr1:154947400-154948800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
35	chr1:154947400-154948800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
36	chr1:154947400-154949000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:154947400-154949200	Flanking Active TSS	Primary B cells from cord blood	blood
38	chr1:154947600-154948800	Flanking Active TSS	Fetal Brain Female	brain
39	chr1:154947600-154949200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr1:154947600-154949600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:154947800-154948800	Flanking Active TSS	Primary T cells from cord blood	blood
42	chr1:154947800-154948800	Flanking Active TSS	Thymus	Thymus
43	chr1:154948000-154948800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
44	chr1:154948000-154948800	Flanking Active TSS	Adipose Nuclei	Adipose
45	chr1:154948000-154949000	Active TSS	Brain Anterior Caudate	brain
46	chr1:154948000-154949200	Transcr. at gene 5' and 3'	Dnd41	blood
47	chr1:154948000-154949400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr1:154948200-154948800	Flanking Active TSS	Fetal Brain Male	brain
49	chr1:154948200-154948800	Active TSS	HepG2	liver
50	chr1:154948200-154949000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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