Variant report

Variant	rs12141529
Chromosome Location	chr1:47902886-47902887
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	MTA3	chr1:47901994-47902922	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:47902127-47903588	GM12878	blood:	n/a	n/a
3	POLR2A	chr1:47902800-47903644	GM12878	blood:	n/a	n/a
4	CTCF	chr1:47901969-47903966	A549	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
5	SIN3A	chr1:47902874-47903634	GM12878	blood:	n/a	chr1:47902880-47902893 chr1:47902881-47902892
6	CTCF	chr1:47902083-47903846	IMR90	lung:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652 chr1:47902578-47902591
7	TCF7L2	chr1:47902190-47903850	HCT-116	colon:	n/a	n/a
8	ELF1	chr1:47902073-47903938	K562	blood:	n/a	chr1:47903423-47903436 chr1:47903588-47903600 chr1:47903133-47903145 chr1:47903288-47903300 chr1:47903322-47903331 chr1:47903787-47903796 chr1:47903785-47903797 chr1:47903292-47903301 chr1:47903793-47903802 chr1:47903655-47903667 chr1:47903784-47903793 chr1:47903788-47903800 chr1:47903315-47903327
9	CTCF	chr1:47902860-47903010	HUVEC	blood vessel:	n/a	n/a
10	RCOR1	chr1:47901790-47903838	K562	blood:	n/a	n/a
11	POLR2A	chr1:47902754-47903955	K562	blood:	n/a	n/a
12	UBTF	chr1:47902126-47904027	K562	blood:	n/a	n/a
13	ZBTB7A	chr1:47902143-47904182	K562	blood:	n/a	chr1:47903645-47903654
14	MAX	chr1:47902072-47903880	NB4	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
15	POLR2A	chr1:47902034-47904062	HEK293	kidney:	n/a	n/a
16	POLR2A	chr1:47901959-47902920	HCT-116	colon:	n/a	n/a
17	CTCF	chr1:47902820-47902970	GM12871	blood:	n/a	n/a
18	CTCF	chr1:47902820-47902970	GM12875	blood:	n/a	n/a
19	CHD1	chr1:47902881-47903637	GM12878	blood:	n/a	chr1:47903380-47903390
20	POLR2A	chr1:47902066-47903914	Hela-S3	cervix:	n/a	n/a
21	MAX	chr1:47902080-47904090	HepG2	liver:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
22	CREB1	chr1:47902014-47904068	HepG2	liver:	n/a	n/a
23	POLR2A	chr1:47902209-47903023	Hela-S3	cervix:	n/a	n/a
24	CCNT2	chr1:47902133-47904058	K562	blood:	n/a	chr1:47903693-47903702
25	CTCF	chr1:47902845-47902913	GM19238	blood:	n/a	n/a
26	MAZ	chr1:47901897-47903976	GM12878	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
27	POLR2A	chr1:47902171-47903941	NB4	blood:	n/a	n/a
28	SIN3AK20	chr1:47902531-47904036	PANC-1	pancreas:	n/a	n/a
29	MAX	chr1:47902742-47903952	A549	lung:	n/a	chr1:47903585-47903595 chr1:47903694-47903704
30	RUNX3	chr1:47902722-47903857	GM12878	blood:	n/a	n/a
31	MYC	chr1:47902116-47903922	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
32	CTCF	chr1:47902758-47903820	GM12892	blood:	n/a	chr1:47903695-47903708 chr1:47903638-47903654 chr1:47903640-47903649 chr1:47903639-47903660 chr1:47903640-47903653 chr1:47903637-47903655 chr1:47903640-47903653 chr1:47903642-47903652
33	POLR2A	chr1:47902857-47903913	GM12878	blood:	n/a	n/a
34	MYC	chr1:47902045-47903986	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
35	CTCF	chr1:47902860-47903010	AG04449	skin:	n/a	n/a
36	SMC3	chr1:47901894-47903047	SK-N-SH	brain:	n/a	chr1:47902581-47902591
37	POLR2A	chr1:47902879-47903698	GM18526	blood:	n/a	n/a
38	CHD2	chr1:47902174-47903867	Hela-S3	cervix:	n/a	chr1:47903702-47903712 chr1:47903380-47903390
39	POLR2A	chr1:47902665-47903009	HepG2	liver:	n/a	n/a
40	E2F4	chr1:47902147-47903868	K562	blood:	n/a	chr1:47903704-47903713 chr1:47903791-47903801 chr1:47902892-47902907 chr1:47903192-47903202 chr1:47903693-47903702 chr1:47903334-47903345 chr1:47903788-47903798 chr1:47903785-47903795
41	UBTF	chr1:47901972-47903997	K562	blood:	n/a	n/a
42	SUZ12	chr1:47901979-47905648	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr1:47902068-47904127	K562	blood:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
44	POLR2A	chr1:47902219-47903821	GM19193	blood:	n/a	n/a
45	CTCF	chr1:47902860-47903010	HBMEC	blood vessel:	n/a	n/a
46	ZBTB7A	chr1:47902190-47903090	K562	blood:	n/a	n/a
47	HA-E2F1	chr1:47902210-47903731	MCF-7	breast:	n/a	chr1:47903704-47903713 chr1:47902892-47902907 chr1:47903192-47903202 chr1:47903693-47903702
48	MAX	chr1:47902169-47903837	Hela-S3	cervix:	n/a	chr1:47903585-47903595 chr1:47903694-47903704 chr1:47902435-47902445
49	RFX5	chr1:47902827-47903225	HepG2	liver:	n/a	n/a
50	HMGN3	chr1:47902729-47904110	K562	blood:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:47902846-47902896	GM12891	blood:	n/a
2	chr1:47902846-47902896	HUVEC	blood vessel:	n/a
3	chr1:47902846-47902896	ovcar-3	ovarian:	n/a
4	chr1:47902846-47902896	PFSK-1	brain:	n/a
5	chr1:47902846-47902896	HPAEpiC	pulmonary alveolar:	n/a
6	chr1:47902846-47902896	GM12878	blood:	n/a
7	chr1:47902846-47902896	ProgFib	skin:	n/a
8	chr1:47902846-47902896	GM19239	blood:	n/a
9	chr1:47902846-47902896	K562	blood:	n/a
10	chr1:47902846-47902896	NHBE	bronchial:	n/a
11	chr1:47902846-47902896	MCF10A-Er-Src	breast:	n/a
12	chr1:47902846-47902896	HEK293	kidney:	embryo
13	chr1:47902846-47902896	HCM	heart:	n/a
14	chr1:47902846-47902896	Hepatocyte	liver:	n/a
15	chr1:47902846-47902896	AG09319	gingival:	n/a
16	chr1:47902846-47902896	HepG2	liver:	n/a
17	chr1:47902846-47902896	GM12892	blood:	n/a
18	chr1:47902846-47902896	A549	lung:	n/a
19	chr1:47902846-47902896	IMR90	lung:	fetal
20	chr1:47902846-47902896	AG04450	lung:	fetal
21	chr1:47902846-47902896	H1-hESC	embryonic stem cell:	embryo
22	chr1:47902846-47902896	SK-N-MC	brain:	n/a
23	chr1:47902846-47902896	HRE	kidney:	n/a
24	chr1:47902846-47902896	T-47D	breast:	n/a
25	chr1:47902846-47902896	SAEC	small airway:	n/a
26	chr1:47902846-47902896	NHDF-neo	bronchial:	n/a
27	chr1:47902846-47902896	Jurkat	blood:	n/a
28	chr1:47902846-47902896	U87	brain:	n/a
29	chr1:47902846-47902896	NB4	blood:	n/a
30	chr1:47902846-47902896	ECC-1	luminal epithelium:	n/a
31	chr1:47902846-47902896	LNCaP	prostate:	n/a
32	chr1:47902846-47902896	HCPEpiC	choroid plexus:	n/a
33	chr1:47902846-47902896	RPTEC	kidney:	n/a
34	chr1:47902846-47902896	HL-60	blood:	n/a
35	chr1:47902846-47902896	HCF	heart:	n/a
36	chr1:47902846-47902896	BE2_C	brain:	n/a
37	chr1:47902846-47902896	GM06990	blood:	n/a
38	chr1:47902846-47902896	CMK	blood:	n/a
39	chr1:47902846-47902896	PANC-1	pancreas:	n/a
40	chr1:47902846-47902896	SK-N-SH_RA	brain:	n/a
41	chr1:47902846-47902896	NT2-D1	testis:	n/a
42	chr1:47902846-47902896	HAEpiC	amniotic membrane:	n/a
43	chr1:47902846-47902896	NH-A	brain:	n/a
44	chr1:47902846-47902896	HNPCEpiC	eye:	n/a
45	chr1:47902846-47902896	HCT-116	colon:	n/a
46	chr1:47902846-47902896	SK-N-SH	brain:	n/a
47	chr1:47902846-47902896	HMEC	breast:	n/a
48	chr1:47902846-47902896	PrEC	prostate:	n/a
49	chr1:47902846-47902896	HIPEpiC	eye:	n/a
50	chr1:47902846-47902896	AG10803	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:47901774..47903783-chr1:47905502..47907193,2	MCF-7	breast:
2	chr1:47901790..47903824-chr1:48190200..48191775,2	K562	blood:
3	chr1:47894501..47897089-chr1:47902727..47904976,2	MCF-7	breast:
4	chr1:47902221..47904815-chr1:47929260..47931018,2	K562	blood:
5	chr1:47902573..47903219-chr14:100274224..100274724,2	Hela-S3	cervix:
6	chr1:47902455..47903363-chr10:89577216..89577997,2	Hela-S3	cervix:
7	chr1:47901999..47903599-chr1:48174794..48176429,2	MCF-7	breast:
8	chr1:47902477..47903371-chr9:131218074..131218707,2	Hela-S3	cervix:
9	chr1:47902492..47903033-chr5:172194621..172195178,2	Hela-S3	cervix:
10	chr1:47902027..47902996-chr1:47935255..47935856,2	K562	blood:
11	chr1:47902862..47904142-chr1:48175786..48176848,4	K562	blood:

Variant related genes	Relation type
FOXD2-AS1	TF binding region
FOXD2-AS1	CpG island
ENSG00000136811	Chromatin interaction
ENSG00000223820	Chromatin interaction
ENSG00000138138	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10218615	0.90[AFR][1000 genomes]
rs10890480	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11211533	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11588964	0.85[AFR][1000 genomes]
rs12065137	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12080109	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12735320	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12751405	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12759377	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1572546	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2098	0.85[AFR][1000 genomes]
rs4480403	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6665067	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6670458	0.88[AFR][1000 genomes]
rs6691723	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7525802	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7528075	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871961	chr1:47875627-47912628	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv534956	chr1:47882277-47905486	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv534957	chr1:47882277-47907965	Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv1001779	chr1:47884229-48111485	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv871299	chr1:47889417-48057890	Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	esv3432093	chr1:47901465-47906063	Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	esv3406880	chr1:47901890-47905238	Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	6 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	chr1:47899000-47904400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr1:47901400-47908000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
3	chr1:47901800-47903200	Flanking Active TSS	Liver	Liver
4	chr1:47901800-47903200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
5	chr1:47901800-47904000	Bivalent/Poised TSS	Brain Inferior Temporal Lobe	brain
6	chr1:47901800-47904600	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:47902000-47903000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
8	chr1:47902000-47903000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr1:47902000-47903200	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr1:47902000-47903200	Bivalent/Poised TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:47902000-47903200	Flanking Active TSS	HUVEC	blood vessel
12	chr1:47902000-47903600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr1:47902000-47904400	Bivalent/Poised TSS	Brain Anterior Caudate	brain
14	chr1:47902000-47904400	Active TSS	A549	lung
15	chr1:47902000-47904800	Active TSS	Sigmoid Colon	Sigmoid Colon
16	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
17	chr1:47902200-47903000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
18	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
19	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
20	chr1:47902200-47903000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
21	chr1:47902200-47903200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
22	chr1:47902200-47903200	Flanking Active TSS	Spleen	Spleen
23	chr1:47902200-47903600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:47902200-47904000	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:47902200-47904000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr1:47902200-47904000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
27	chr1:47902200-47904000	Active TSS	Hela-S3	cervix
28	chr1:47902200-47904200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr1:47902200-47904200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:47902200-47904200	Active TSS	HMEC	breast
31	chr1:47902200-47904200	Active TSS	K562	blood
32	chr1:47902200-47904400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr1:47902200-47904400	Active TSS	HSMM	muscle
34	chr1:47902200-47904400	Active TSS	NHLF	lung
35	chr1:47902200-47904600	Active TSS	Small Intestine	intestine
36	chr1:47902200-47905000	Active TSS	Aorta	Aorta
37	chr1:47902200-47906000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr1:47902400-47903000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
39	chr1:47902400-47903000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
40	chr1:47902400-47903000	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
41	chr1:47902400-47903000	Flanking Active TSS	Lung	lung
42	chr1:47902400-47903000	Flanking Active TSS	Pancreas	Pancrea
43	chr1:47902400-47903000	Transcr. at gene 5' and 3'	Right Atrium	heart
44	chr1:47902400-47903400	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr1:47902400-47903400	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr1:47902400-47903400	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
47	chr1:47902400-47903600	Bivalent/Poised TSS	Brain Angular Gyrus	brain
48	chr1:47902400-47903800	Active TSS	Esophagus	oesophagus
49	chr1:47902400-47903800	Active TSS	Dnd41	blood
50	chr1:47902400-47904000	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived

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