Variant report

Variant	rs28364800
Chromosome Location	chr1:47069894-47069895
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	POLR2A	chr1:47069302-47071281	GM12878	blood:	n/a	n/a
2	ETS1	chr1:47069555-47069987	K562	blood:	n/a	chr1:47069974-47069985 chr1:47069776-47069787
3	TRIM28	chr1:47069731-47070295	K562	blood:	n/a	n/a
4	STAT1	chr1:47069738-47070334	GM12878	blood:	n/a	chr1:47070124-47070135 chr1:47070222-47070230
5	POLR2A	chr1:47069462-47070243	GM12878	blood:	n/a	n/a
6	MAZ	chr1:47069596-47070354	GM12878	blood:	n/a	n/a
7	CTCF	chr1:47069682-47069917	MCF-7	breast:	n/a	chr1:47069773-47069786 chr1:47069771-47069789
8	POLR2A	chr1:47069551-47070342	K562	blood:	n/a	n/a
9	NRF1	chr1:47069788-47070259	H1-hESC	embryonic stem cell:	n/a	chr1:47070050-47070059 chr1:47069987-47070001 chr1:47069987-47069998 chr1:47070047-47070061 chr1:47069984-47069998 chr1:47069987-47069998 chr1:47070050-47070061
10	POLR2A	chr1:47069152-47071237	GM12878	blood:	n/a	n/a
11	ELF1	chr1:47069568-47070082	A549	lung:	n/a	chr1:47069917-47069930
12	POLR2A	chr1:47069398-47070433	HUVEC	blood vessel:	n/a	n/a
13	IRF1	chr1:47069407-47070291	K562	blood:	n/a	chr1:47070121-47070135 chr1:47069975-47069989 chr1:47070068-47070082 chr1:47069646-47069660 chr1:47070123-47070134
14	YY1	chr1:47069486-47070251	GM12878	blood:	n/a	chr1:47069630-47069652
15	ELF1	chr1:47069472-47070201	K562	blood:	n/a	chr1:47069917-47069930
16	GTF2F1	chr1:47069193-47070203	K562	blood:	n/a	n/a
17	SMARCB1	chr1:47069480-47070248	Hela-S3	cervix:	n/a	n/a
18	TEAD4	chr1:47069395-47070375	K562	blood:	n/a	n/a
19	TFAP2C	chr1:47069414-47070478	Hela-S3	cervix:	n/a	chr1:47070015-47070030
20	POLR2A	chr1:47069533-47070293	HL-60	blood:	n/a	n/a
21	TBL1XR1	chr1:47069665-47070282	K562	blood:	n/a	n/a
22	YY1	chr1:47069529-47069922	GM12891	blood:	n/a	chr1:47069630-47069652
23	EGR1	chr1:47069320-47070500	HCT-116	colon:	n/a	chr1:47069971-47069984 chr1:47069988-47069997 chr1:47069972-47069986 chr1:47069970-47069985 chr1:47070166-47070176 chr1:47069971-47069984 chr1:47069971-47069984
24	TCF7L2	chr1:47069314-47070185	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr1:47069532-47070265	A549	lung:	n/a	n/a
26	CTCF	chr1:47069576-47069971	K562	blood:	n/a	chr1:47069773-47069786 chr1:47069771-47069789
27	POLR2A	chr1:47069607-47070261	HepG2	liver:	n/a	n/a
28	SP1	chr1:47069638-47070239	GM12878	blood:	n/a	chr1:47070070-47070079 chr1:47069975-47069987 chr1:47069654-47069668 chr1:47069926-47069937 chr1:47069945-47069956 chr1:47069975-47069987 chr1:47069976-47069985 chr1:47070018-47070032 chr1:47070065-47070079 chr1:47069972-47069986 chr1:47069977-47069986 chr1:47069649-47069659
29	TAF1	chr1:47069604-47070273	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr1:47069487-47070313	K562	blood:	n/a	n/a
31	ELK1	chr1:47069722-47070317	K562	blood:	n/a	n/a
32	PML	chr1:47069570-47070102	K562	blood:	n/a	n/a
33	ZC3H11A	chr1:47069540-47070278	K562	blood:	n/a	n/a
34	ZNF143	chr1:47069684-47070255	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:47069566-47070330	HCT-116	colon:	n/a	n/a
36	GABPA	chr1:47069578-47070186	K562	blood:	n/a	chr1:47070050-47070059 chr1:47069987-47070001 chr1:47070047-47070061 chr1:47069984-47069998 chr1:47069987-47069998 chr1:47070050-47070061
37	HCFC1	chr1:47068857-47070468	Hela-S3	cervix:	n/a	n/a
38	ELF1	chr1:47069726-47070134	HepG2	liver:	n/a	chr1:47069917-47069930
39	CEBPD	chr1:47069674-47070270	HepG2	liver:	n/a	n/a
40	POLR2A	chr1:47069681-47070234	HUVEC	blood vessel:	n/a	n/a
41	POLR2A	chr1:47069576-47070122	H1-neurons	neurons:	n/a	n/a
42	YY1	chr1:47069518-47070179	K562	blood:	n/a	chr1:47069630-47069652
43	CTCF	chr1:47069760-47069910	HPAF	blood vessel:	n/a	chr1:47069773-47069786 chr1:47069771-47069789
44	CHD2	chr1:47069548-47070152	GM12878	blood:	n/a	n/a
45	POLR2A	chr1:47069464-47070512	SK-N-MC	brain:	n/a	n/a
46	IRF1	chr1:47069623-47070306	K562	blood:	n/a	chr1:47070121-47070135 chr1:47069975-47069989 chr1:47070068-47070082 chr1:47069646-47069660 chr1:47070123-47070134
47	RCOR1	chr1:47069380-47070448	Hela-S3	cervix:	n/a	n/a
48	YY1	chr1:47069518-47070227	K562	blood:	n/a	chr1:47069630-47069652
49	MAX	chr1:47069657-47070031	HepG2	liver:	n/a	n/a
50	POLR2A	chr1:47069386-47070324	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47069390..47072755-chr1:47079314..47082367,4	MCF-7	breast:
2	chr1:47068429..47072503-chr1:47081068..47085092,4	MCF-7	breast:
3	chr1:47033343..47035201-chr1:47067108..47069992,2	K562	blood:

Variant related genes	Relation type
MKNK1	TF binding region
ENSG00000142961	Chromatin interaction
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11211305	0.84[ASN][1000 genomes]
rs12095096	0.84[ASN][1000 genomes]
rs12096548	0.84[ASN][1000 genomes]
rs2273935	0.90[AMR][1000 genomes]
rs3737734	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3737735	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3753358	1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3766235	0.84[ASN][1000 genomes]
rs3766237	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3766238	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3766239	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3766242	0.81[AMR][1000 genomes]
rs3766244	0.90[AMR][1000 genomes]
rs55849859	0.90[AMR][1000 genomes]
rs56195429	0.90[AMR][1000 genomes]
rs56228418	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs56939666	0.81[AMR][1000 genomes]
rs61734408	0.81[AMR][1000 genomes]
rs6703563	0.84[ASN][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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 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	chr1:47068800-47070400	Active TSS	HSMM	muscle
2	chr1:47068800-47070600	Active TSS	NHLF	lung
3	chr1:47069000-47070200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:47069000-47070200	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr1:47069000-47070400	Active TSS	ES-I3 Cell Line	embryonic stem cell
6	chr1:47069000-47070400	Active TSS	HUES48 Cell Line	embryonic stem cell
7	chr1:47069000-47070400	Active TSS	Colonic Mucosa	Colon
8	chr1:47069000-47070400	Active TSS	A549	lung
9	chr1:47069000-47070800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:47069000-47071200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:47069200-47070000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr1:47069200-47070000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:47069200-47070000	Active TSS	Small Intestine	intestine
14	chr1:47069200-47070200	Active TSS	Primary T killer memory cells from peripheral blood	blood
15	chr1:47069200-47070200	Active TSS	Rectal Mucosa Donor 29	rectum
16	chr1:47069200-47070400	Active TSS	H9 Cell Line	embryonic stem cell
17	chr1:47069200-47070400	Active TSS	Colon Smooth Muscle	Colon
18	chr1:47069200-47070400	Active TSS	Fetal Kidney	kidney
19	chr1:47069200-47070600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:47069200-47070600	Active TSS	Aorta	Aorta
21	chr1:47069200-47070600	Active TSS	Ovary	ovary
22	chr1:47069200-47070800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:47069400-47070000	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr1:47069400-47070000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:47069400-47070000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
26	chr1:47069400-47070000	Active TSS	Placenta Amnion	Placenta Amnion
27	chr1:47069400-47070000	Active TSS	Stomach Mucosa	stomach
28	chr1:47069400-47070200	Active TSS	iPS-20b Cell Line	embryonic stem cell
29	chr1:47069400-47070200	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:47069400-47070200	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr1:47069400-47070200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:47069400-47070200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr1:47069400-47070200	Active TSS	Liver	Liver
34	chr1:47069400-47070200	Active TSS	Fetal Intestine Large	intestine
35	chr1:47069400-47070200	Active TSS	Gastric	stomach
36	chr1:47069400-47070200	Active TSS	Sigmoid Colon	Sigmoid Colon
37	chr1:47069400-47070200	Active TSS	Monocytes-CD14+_RO01746	blood
38	chr1:47069400-47070200	Active TSS	NHEK	skin
39	chr1:47069400-47070400	Active TSS	H1 Cell Line	embryonic stem cell
40	chr1:47069400-47070400	Active TSS	HUES6 Cell Line	embryonic stem cell
41	chr1:47069400-47070400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:47069400-47070400	Active TSS	iPS-15b Cell Line	embryonic stem cell
43	chr1:47069400-47070400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr1:47069400-47070400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr1:47069400-47070400	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr1:47069400-47070400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr1:47069400-47070400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:47069400-47070400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr1:47069400-47070400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr1:47069400-47070400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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