Variant report

Variant	rs552446
Chromosome Location	chr1:153505572-153505573
allele	A/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	ZBTB7A	chr1:153505538-153506136	ECC-1	luminal epithelium:	n/a	n/a
2	PBX3	chr1:153505314-153506846	SK-N-SH	brain:	n/a	n/a
3	TCF12	chr1:153505534-153506114	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr1:153504001-153509011	U87	brain:	n/a	n/a
5	POLR2A	chr1:153504109-153508508	A549	lung:	n/a	n/a
6	POLR2A	chr1:153505145-153509494	Hela-S3	cervix:	n/a	n/a
7	SIN3A	chr1:153505296-153506129	H1-hESC	embryonic stem cell:	n/a	n/a
8	POLR2A	chr1:153505510-153505910	K562	blood:	n/a	n/a
9	SP1	chr1:153505368-153506836	A549	lung:	n/a	chr1:153506427-153506437 chr1:153505389-153505398 chr1:153506427-153506436 chr1:153506428-153506437 chr1:153506693-153506702 chr1:153506427-153506436
10	TFAP2C	chr1:153505386-153507077	Hela-S3	cervix:	n/a	n/a
11	POLR2A	chr1:153505214-153506163	MCF-7	breast:	n/a	n/a
12	POLR2A	chr1:153505307-153509454	Hela-S3	cervix:	n/a	n/a
13	CEBPB	chr1:153505390-153505977	H1-hESC	embryonic stem cell:	n/a	n/a
14	POLR2A	chr1:153505520-153505589	HepG2	liver:	n/a	n/a
15	POLR2A	chr1:153505192-153509569	HCT-116	colon:	n/a	n/a
16	CTCF	chr1:153505492-153505991	MCF-7	breast:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
17	MAZ	chr1:153504643-153509324	IMR90	lung:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
18	MAX	chr1:153505450-153509582	HCT-116	colon:	n/a	chr1:153506458-153506465 chr1:153508744-153508753 chr1:153506973-153506982 chr1:153509221-153509231 chr1:153506972-153506981 chr1:153509055-153509062 chr1:153508744-153508753
19	CHD2	chr1:153505478-153505901	K562	blood:	n/a	n/a
20	CTCF	chr1:153505569-153505995	K562	blood:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
21	CTCF	chr1:153505563-153505950	A549	lung:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
22	SP1	chr1:153505226-153506047	H1-hESC	embryonic stem cell:	n/a	chr1:153505389-153505398
23	RAD21	chr1:153505301-153505998	H1-hESC	embryonic stem cell:	n/a	chr1:153505323-153505336 chr1:153505773-153505792
24	JUND	chr1:153505349-153505983	H1-hESC	embryonic stem cell:	n/a	n/a
25	RAD21	chr1:153505508-153506963	IMR90	lung:	n/a	chr1:153505773-153505792
26	JUND	chr1:153505492-153506847	A549	lung:	n/a	chr1:153506399-153506406 chr1:153506396-153506407
27	SMC3	chr1:153505569-153505967	GM12878	blood:	n/a	chr1:153505774-153505788
28	CEBPB	chr1:153505401-153506850	A549	lung:	n/a	n/a
29	CTCF	chr1:153505460-153505610	HEK293	kidney:	n/a	chr1:153505476-153505484
30	SIN3AK20	chr1:153505416-153506776	A549	lung:	n/a	n/a
31	POLR2A	chr1:153505437-153506814	MCF10A-Er-Src	breast:	n/a	n/a
32	RAD21	chr1:153505508-153506170	ECC-1	luminal epithelium:	n/a	chr1:153505773-153505792
33	RAD21	chr1:153505546-153505969	MCF-7	breast:	n/a	chr1:153505773-153505792
34	YY1	chr1:153505471-153506062	H1-hESC	embryonic stem cell:	n/a	n/a
35	POLR2A	chr1:153505198-153509437	Hela-S3	cervix:	n/a	n/a
36	POLR2A	chr1:153505162-153509201	SK-N-SH	brain:	n/a	n/a
37	POLR2A	chr1:153505225-153509006	ProgFib	skin:	n/a	n/a
38	RAD21	chr1:153505537-153506634	Hela-S3	cervix:	n/a	chr1:153505773-153505792
39	CHD2	chr1:153505437-153507025	Hela-S3	cervix:	n/a	n/a
40	TCF7L2	chr1:153505258-153506096	PANC-1	pancreas:	n/a	n/a
41	BCL3	chr1:153505257-153506994	A549	lung:	n/a	chr1:153505748-153505761 chr1:153506972-153506981 chr1:153506398-153506407 chr1:153506973-153506982
42	RAD21	chr1:153505308-153506983	HCT-116	colon:	n/a	chr1:153505323-153505336 chr1:153505773-153505792
43	SMARCB1	chr1:153505278-153507019	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr1:153505568-153505941	T-47D	breast:	n/a	chr1:153505773-153505789 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788
45	POLR2A	chr1:153505262-153506881	Gliobla	brain:	n/a	n/a
46	PBX3	chr1:153505178-153506863	A549	lung:	n/a	n/a
47	TBP	chr1:153505348-153505912	H1-hESC	embryonic stem cell:	n/a	n/a
48	SIN3AK20	chr1:153505209-153507034	PANC-1	pancreas:	n/a	n/a
49	RAD21	chr1:153505447-153506555	A549	lung:	n/a	chr1:153505773-153505792
50	CTCF	chr1:153505362-153506495	HCT-116	colon:	n/a	chr1:153505773-153505789 chr1:153505476-153505484 chr1:153505772-153505790 chr1:153505774-153505795 chr1:153505775-153505788

No.	Distal block	Cell Line	Cell type
1	chr1:153503911..153505890-chr1:153631477..153634216,2	K562	blood:
2	chr1:153505459..153506316-chr6:26199169..26200064,2	Hela-S3	cervix:
3	chr1:153505342..153508148-chr1:153641864..153643367,2	MCF-7	breast:
4	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:
5	chr1:153504897..153511307-chr1:153536318..153542519,37	MCF-7	breast:
6	chr1:153504329..153507150-chr1:153606463..153608211,3	MCF-7	breast:
7	chr1:153504925..153506891-chr1:153507588..153509186,2	K562	blood:
8	chr1:153504456..153510099-chr1:153538941..153542898,8	K562	blood:
9	chr1:153504127..153510657-chr1:153537210..153543304,15	K562	blood:
10	chr1:153504209..153505838-chr1:153511280..153513163,2	K562	blood:
11	chr1:153505312..153506366-chr1:153540363..153541887,16	K562	blood:
12	chr1:153467541..153469828-chr1:153502709..153505691,2	K562	blood:
13	chr1:153485879..153486801-chr1:153505033..153505646,2	K562	blood:
14	chr1:153503567..153510701-chr1:153536906..153541884,20	MCF-7	breast:
15	chr1:153505490..153510008-chr1:153584041..153589482,7	MCF-7	breast:
16	chr1:153502325..153505921-chr1:153601540..153604182,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000238279	TF binding region
ENSG00000197956	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000196866	Chromatin interaction
ENSG00000189171	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000272030	Chromatin interaction
ENSG00000160679	Chromatin interaction
ENSG00000143621	Chromatin interaction
ENSG00000271853	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs17695220	0.86[AMR][1000 genomes]
rs1887039	0.80[AMR][1000 genomes]
rs2094217	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094737	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2094738	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2248745	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2262587	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2339696	0.86[AMR][1000 genomes]
rs2480695	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2480696	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28427870	0.93[ASN][1000 genomes]
rs28464843	0.88[AMR][1000 genomes]
rs28483109	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3762262	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4017737	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4272569	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4430277	0.81[EUR][1000 genomes]
rs477339	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845351	0.83[EUR][1000 genomes]
rs4845352	0.84[EUR][1000 genomes]
rs4845555	0.80[AMR][1000 genomes]
rs532652	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs550597	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs585215	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587743	0.86[AMR][1000 genomes]
rs659403	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659755	0.86[AMR][1000 genomes]
rs6690638	0.80[AMR][1000 genomes]
rs6690712	0.80[AMR][1000 genomes]
rs7515940	0.81[AMR][1000 genomes]
rs7518306	0.83[EUR][1000 genomes]
rs7520093	0.88[AMR][1000 genomes]
rs7534343	0.88[AMR][1000 genomes]
rs7534347	0.88[AMR][1000 genomes]
rs7537898	0.81[AMR][1000 genomes]
rs7544359	0.81[AMR][1000 genomes]
rs9426945	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427239	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9427287	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153489000-153506000	Weak transcription	Gastric	stomach
2	chr1:153498000-153505800	Weak transcription	Aorta	Aorta
3	chr1:153498200-153506000	Weak transcription	Right Ventricle	heart
4	chr1:153501800-153505600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr1:153503400-153507200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr1:153503800-153507400	Enhancers	Small Intestine	intestine
7	chr1:153504000-153505800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:153504000-153506400	Enhancers	Primary T cells from cord blood	blood
9	chr1:153504000-153507600	Enhancers	Fetal Thymus	thymus
10	chr1:153504200-153505800	Enhancers	Esophagus	oesophagus
11	chr1:153504200-153506000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr1:153504200-153506000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:153504200-153506600	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr1:153504200-153507600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr1:153504400-153505600	Enhancers	NHEK	skin
16	chr1:153504400-153505800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:153504400-153506800	Enhancers	Primary B cells from peripheral blood	blood
18	chr1:153504400-153507000	Enhancers	Primary hematopoietic stem cells	blood
19	chr1:153504600-153505600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:153504600-153505600	Enhancers	Colon Smooth Muscle	Colon
21	chr1:153504600-153505800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr1:153504600-153506200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr1:153504600-153506200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr1:153504600-153506400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
25	chr1:153504800-153505600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:153504800-153505600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
27	chr1:153504800-153505600	Enhancers	Placenta	Placenta
28	chr1:153504800-153505600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
29	chr1:153504800-153505600	Flanking Active TSS	A549	lung
30	chr1:153504800-153505800	Enhancers	Placenta Amnion	Placenta Amnion
31	chr1:153504800-153505800	Enhancers	NHLF	lung
32	chr1:153504800-153506000	Enhancers	HMEC	breast
33	chr1:153504800-153506400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
34	chr1:153504800-153506600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr1:153504800-153507200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
36	chr1:153504800-153507200	Enhancers	Spleen	Spleen
37	chr1:153504800-153507800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
38	chr1:153504800-153507800	Flanking Active TSS	Duodenum Mucosa	Duodenum
39	chr1:153504800-153508000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
40	chr1:153505000-153505800	Enhancers	Adipose Nuclei	Adipose
41	chr1:153505000-153506400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr1:153505000-153506400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr1:153505000-153506600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr1:153505000-153506800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr1:153505000-153507000	Flanking Active TSS	Hela-S3	cervix
46	chr1:153505000-153507400	Enhancers	Liver	Liver
47	chr1:153505200-153505600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:153505200-153505600	Active TSS	Breast Myoepithelial Primary Cells	Breast
49	chr1:153505200-153505600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
50	chr1:153505200-153505600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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