Variant report

Variant	rs12757699
Chromosome Location	chr1:86861716-86861717
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	CREB1	chr1:86861414-86862394	GM12878	blood:	n/a	n/a
2	POLR2A	chr1:86861463-86862475	GM18951	blood:	n/a	n/a
3	YY1	chr1:86861588-86862010	GM12878	blood:	n/a	n/a
4	TAF1	chr1:86861463-86862466	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr1:86861558-86862152	GM12878	blood:	n/a	n/a
6	MAX	chr1:86861650-86862345	A549	lung:	n/a	n/a
7	TCF12	chr1:86861506-86862259	ECC-1	luminal epithelium:	n/a	n/a
8	EGR1	chr1:86861519-86861832	K562	blood:	n/a	chr1:86861568-86861581 chr1:86861582-86861592
9	POLR2A	chr1:86860834-86862483	SK-N-MC	brain:	n/a	n/a
10	POLR2A	chr1:86860715-86862399	PANC-1	pancreas:	n/a	n/a
11	NFIC	chr1:86861623-86862152	GM12878	blood:	n/a	n/a
12	POLR2A	chr1:86861136-86862293	HEK293	kidney:	n/a	n/a
13	TAF1	chr1:86861637-86862107	H1-hESC	embryonic stem cell:	n/a	n/a
14	MAX	chr1:86861434-86862398	ECC-1	luminal epithelium:	n/a	n/a
15	YY1	chr1:86861666-86862030	A549	lung:	n/a	n/a
16	ZBTB7A	chr1:86861425-86861847	K562	blood:	n/a	chr1:86861579-86861590
17	MXI1	chr1:86861598-86862116	H1-hESC	embryonic stem cell:	n/a	chr1:86861997-86862012
18	POLR2A	chr1:86861503-86862140	GM12878	blood:	n/a	n/a
19	SIN3AK20	chr1:86861708-86862169	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr1:86861033-86862383	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr1:86861546-86862412	GM12878	blood:	n/a	n/a
22	EGR1	chr1:86861515-86862002	GM12878	blood:	n/a	chr1:86861568-86861581 chr1:86861582-86861592
23	CREB1	chr1:86861487-86862292	ECC-1	luminal epithelium:	n/a	n/a
24	RUNX3	chr1:86861413-86862267	GM12878	blood:	n/a	n/a
25	MAZ	chr1:86861362-86862825	GM12878	blood:	n/a	n/a
26	POLR2A	chr1:86861579-86862200	MCF-7	breast:	n/a	n/a
27	PAX5	chr1:86861667-86862228	GM12891	blood:	n/a	n/a
28	SIN3A	chr1:86861144-86862469	H1-hESC	embryonic stem cell:	n/a	chr1:86862072-86862085
29	REST	chr1:86861360-86862117	PANC-1	pancreas:	n/a	n/a
30	SMARCC1	chr1:86861046-86862370	Hela-S3	cervix:	n/a	n/a
31	ZBTB7A	chr1:86861203-86862017	ECC-1	luminal epithelium:	n/a	chr1:86861579-86861590
32	YY1	chr1:86861548-86862197	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:86861479-86862237	GM12892	blood:	n/a	n/a
34	POLR2A	chr1:86861474-86862183	GM12878	blood:	n/a	n/a
35	POLR2A	chr1:86861467-86862334	HL-60	blood:	n/a	n/a
36	POLR2A	chr1:86861438-86862344	Raji	blood:	n/a	n/a
37	POLR2A	chr1:86861606-86862097	U87	brain:	n/a	n/a
38	POLR2A	chr1:86861430-86862162	Gliobla	brain:	n/a	n/a
39	JUND	chr1:86861701-86861960	H1-hESC	embryonic stem cell:	n/a	n/a
40	MXI1	chr1:86860760-86863066	SK-N-SH	brain:	n/a	chr1:86861997-86862012
41	REST	chr1:86860811-86862757	H1-neurons	neurons:	n/a	chr1:86862115-86862128
42	POLR2A	chr1:86861462-86862161	MCF-7	breast:	n/a	n/a
43	CTCF	chr1:86861620-86861770	GM12867	blood:	n/a	n/a
44	BCLAF1	chr1:86861583-86862074	GM12878	blood:	n/a	n/a
45	MAX	chr1:86861367-86862252	K562	blood:	n/a	n/a
46	POLR2A	chr1:86861436-86862260	GM15510	blood:	n/a	n/a
47	YY1	chr1:86861615-86862221	H1-hESC	embryonic stem cell:	n/a	n/a
48	ATF1	chr1:86861603-86862130	K562	blood:	n/a	n/a
49	ATF2	chr1:86861695-86862033	GM12878	blood:	n/a	n/a
50	MAX	chr1:86861537-86862303	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:86821077..86823352-chr1:86861196..86863227,2	K562	blood:

Variant related genes	Relation type
ODF2L	TF binding region
ENSG00000122417	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12724057	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12733468	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12749637	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs12758659	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1334139	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17129145	1.00[AMR][1000 genomes]
rs17129150	0.82[AMR][1000 genomes]
rs17129169	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs17129194	0.84[AMR][1000 genomes]
rs34204564	0.82[AFR][1000 genomes]
rs34495136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34513089	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34536842	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34834083	0.83[AMR][1000 genomes]
rs34851039	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35261823	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs35303211	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs35408727	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35604082	0.80[AMR][1000 genomes]
rs35908397	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35950578	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs55917045	1.00[AMR][1000 genomes]
rs71662157	0.82[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs71662158	0.82[AMR][1000 genomes]
rs71662160	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71662161	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs932692	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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	nsv546722	chr1:86278315-86891073	Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
2	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv1002541	chr1:86689088-86905902	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 gene(s)	inside rSNPs	diseases
4	nsv871081	chr1:86806372-86892819	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	3 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	chr1:86859600-86862800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr1:86859800-86862200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:86859800-86862400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:86859800-86862800	Active TSS	Pancreatic Islets	Pancreatic Islet
5	chr1:86860200-86862400	Active TSS	HMEC	breast
6	chr1:86860200-86862600	Active TSS	NHLF	lung
7	chr1:86860200-86862800	Active TSS	Right Atrium	heart
8	chr1:86860400-86862400	Active TSS	HUES48 Cell Line	embryonic stem cell
9	chr1:86860400-86862400	Active TSS	NHDF-Ad	bronchial
10	chr1:86860400-86862600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:86860600-86862600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr1:86860800-86862400	Active TSS	HUES64 Cell Line	embryonic stem cell
13	chr1:86860800-86862400	Active TSS	iPS-18 Cell Line	embryonic stem cell
14	chr1:86860800-86862400	Active TSS	Brain Angular Gyrus	brain
15	chr1:86860800-86862400	Active TSS	Brain Inferior Temporal Lobe	brain
16	chr1:86860800-86862400	Active TSS	Esophagus	oesophagus
17	chr1:86860800-86862600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr1:86860800-86862600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:86860800-86862600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr1:86860800-86862600	Active TSS	iPS-20b Cell Line	embryonic stem cell
21	chr1:86860800-86862600	Active TSS	Fetal Intestine Large	intestine
22	chr1:86860800-86862600	Active TSS	Fetal Kidney	kidney
23	chr1:86860800-86862800	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:86860800-86862800	Active TSS	HSMMtube	muscle
25	chr1:86860800-86863000	Active TSS	Colonic Mucosa	Colon
26	chr1:86861000-86862200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr1:86861000-86862200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr1:86861000-86862200	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr1:86861000-86862200	Active TSS	Gastric	stomach
30	chr1:86861000-86862400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr1:86861000-86862400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr1:86861000-86862400	Active TSS	Thymus	Thymus
33	chr1:86861000-86862600	Active TSS	Fetal Muscle Trunk	muscle
34	chr1:86861000-86862600	Active TSS	Left Ventricle	heart
35	chr1:86861000-86862600	Active TSS	Lung	lung
36	chr1:86861000-86862600	Active TSS	Ovary	ovary
37	chr1:86861000-86862600	Active TSS	Pancreas	Pancrea
38	chr1:86861000-86862600	Active TSS	Rectal Smooth Muscle	rectum
39	chr1:86861000-86862600	Active TSS	A549	lung
40	chr1:86861000-86862800	Active TSS	Psoas Muscle	Psoas
41	chr1:86861200-86862200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr1:86861200-86862200	Active TSS	Fetal Intestine Small	intestine
43	chr1:86861200-86862200	Active TSS	Spleen	Spleen
44	chr1:86861200-86862200	Active TSS	HSMM	muscle
45	chr1:86861200-86862200	Active TSS	K562	blood
46	chr1:86861200-86862400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:86861200-86862400	Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr1:86861200-86862400	Active TSS	iPS-15b Cell Line	embryonic stem cell
49	chr1:86861200-86862400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr1:86861200-86862400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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