Variant report

Variant	rs12075911
Chromosome Location	chr1:84543276-84543277
allele	A/C
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	CCNT2	chr1:84543165-84544195	K562	blood:	n/a	chr1:84543960-84543969
2	GABPA	chr1:84543042-84543882	SK-N-SH	brain:	n/a	n/a
3	TAF1	chr1:84543182-84543673	A549	lung:	n/a	n/a
4	ETS1	chr1:84543144-84543619	K562	blood:	n/a	chr1:84543482-84543495 chr1:84543601-84543612
5	HEY1	chr1:84543060-84543700	K562	blood:	n/a	chr1:84543529-84543544 chr1:84543640-84543655
6	POLR2A	chr1:84543032-84543968	HCT-116	colon:	n/a	n/a
7	POLR2A	chr1:84543051-84544048	ECC-1	luminal epithelium:	n/a	n/a
8	MAX	chr1:84542943-84543742	SK-N-SH	brain:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
9	POLR2A	chr1:84543024-84544026	GM12891	blood:	n/a	n/a
10	RAD21	chr1:84543103-84543565	Hela-S3	cervix:	n/a	n/a
11	GABPA	chr1:84543094-84544099	K562	blood:	n/a	n/a
12	POLR2A	chr1:84542986-84544447	Hela-S3	cervix:	n/a	n/a
13	BCLAF1	chr1:84543128-84543608	GM12878	blood:	n/a	chr1:84543570-84543579
14	POLR2A	chr1:84543250-84543923	HUVEC	blood vessel:	n/a	n/a
15	HEY1	chr1:84543045-84543875	HepG2	liver:	n/a	chr1:84543529-84543544 chr1:84543640-84543655
16	POLR2A	chr1:84543236-84543756	SK-N-MC	brain:	n/a	n/a
17	MAX	chr1:84543002-84544430	K562	blood:	n/a	chr1:84543151-84543161 chr1:84543360-84543369 chr1:84544133-84544143
18	BACH1	chr1:84543125-84543656	H1-hESC	embryonic stem cell:	n/a	n/a
19	POLR2A	chr1:84543116-84543863	K562	blood:	n/a	n/a
20	POLR2A	chr1:84543254-84544272	HepG2	liver:	n/a	n/a
21	CTCF	chr1:84543200-84543350	HMF	breast:	n/a	n/a
22	MYC	chr1:84543092-84543631	HepG2	liver:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
23	POLR2A	chr1:84543085-84543668	GM12891	blood:	n/a	n/a
24	TAF1	chr1:84543113-84543852	K562	blood:	n/a	n/a
25	MAX	chr1:84542945-84544346	NB4	blood:	n/a	chr1:84543151-84543161 chr1:84543360-84543369 chr1:84544133-84544143
26	POLR2A	chr1:84543216-84543860	HepG2	liver:	n/a	n/a
27	REST	chr1:84543231-84543432	K562	blood:	n/a	n/a
28	TCF7L2	chr1:84543219-84543751	PANC-1	pancreas:	n/a	n/a
29	GTF2F1	chr1:84543035-84543694	K562	blood:	n/a	n/a
30	MYC	chr1:84542974-84543827	MCF10A-Er-Src	breast:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
31	MAFK	chr1:84543117-84543475	HepG2	liver:	n/a	n/a
32	RAD21	chr1:84543056-84543546	IMR90	lung:	n/a	n/a
33	GABPA	chr1:84543274-84543757	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr1:84543116-84543603	GM12892	blood:	n/a	n/a
35	HCFC1	chr1:84542987-84543859	K562	blood:	n/a	n/a
36	POLR2A	chr1:84543146-84543988	HepG2	liver:	n/a	n/a
37	ETS1	chr1:84543120-84543892	K562	blood:	n/a	chr1:84543482-84543495 chr1:84543635-84543644 chr1:84543637-84543646 chr1:84543635-84543644 chr1:84543635-84543651 chr1:84543635-84543644 chr1:84543635-84543644 chr1:84543633-84543643 chr1:84543635-84543644 chr1:84543601-84543612 chr1:84543634-84543647
38	ZBTB7A	chr1:84543051-84544273	ECC-1	luminal epithelium:	n/a	n/a
39	MXI1	chr1:84543005-84544827	IMR90	lung:	n/a	n/a
40	ELF1	chr1:84543055-84544451	GM12878	blood:	n/a	chr1:84544159-84544171 chr1:84543570-84543582 chr1:84543604-84543616
41	POLR2A	chr1:84543264-84544003	HUVEC	blood vessel:	n/a	n/a
42	HMGN3	chr1:84543146-84544289	K562	blood:	n/a	n/a
43	POLR2A	chr1:84543145-84544121	MCF-7	breast:	n/a	n/a
44	BCL3	chr1:84543200-84543635	A549	lung:	n/a	chr1:84543570-84543579
45	RAD21	chr1:84543078-84543809	SK-N-SH_RA	brain:	n/a	chr1:84543583-84543595
46	POLR2A	chr1:84543246-84543709	GM12892	blood:	n/a	n/a
47	POLR2A	chr1:84543215-84544017	HCT-116	colon:	n/a	n/a
48	CREB1	chr1:84543166-84543932	K562	blood:	n/a	n/a
49	CTCF	chr1:84543180-84543330	RPTEC	kidney:	n/a	n/a
50	PAX5	chr1:84543165-84543946	GM12892	blood:	n/a	chr1:84543647-84543656 chr1:84543643-84543652

No.	Distal block	Cell Line	Cell type
1	chr1:84463410..84466364-chr1:84542152..84546505,5	K562	blood:
2	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
3	chr1:84542242..84543745-chr1:85154770..85157524,2	K562	blood:
4	chr1:84542977..84543701-chr9:140135375..140136244,2	Hela-S3	cervix:
5	chr1:84387778..84389882-chr1:84541236..84543359,2	K562	blood:
6	chr1:84540590..84543508-chr1:84558962..84560991,2	K562	blood:
7	chr1:84541598..84548799-chr1:84549003..84554628,15	K562	blood:
8	chr1:84377090..84379247-chr1:84542414..84544902,2	K562	blood:
9	chr1:84542759..84543477-chr10:17272146..17272948,2	Hela-S3	cervix:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TTLL7-3	chr1:84542062-84543325	XLOC_000889
2	lnc-TTLL7-3	chr1:84542014-84543614	ENSG00000271576.1
3	lnc-TTLL7-3	chr1:84542014-84543655	NONHSAT004184

Variant related genes	Relation type
PRKACB	TF binding region
ENSG00000117155	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000137941	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000188229	Chromatin interaction
ENSG00000213540	Chromatin interaction
ENSG00000026025	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs11163896	1.00[AMR][1000 genomes]
rs12059074	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12062467	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12064346	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069372	1.00[AMR][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	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv871655	chr1:84517261-84550849	Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv546689	chr1:84531117-84670816	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	esv3379138	chr1:84531980-84545128	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	esv3411922	chr1:84542914-84544812	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 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	chr1:84542000-84544600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:84542000-84544800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:84542000-84545200	Active TSS	HUES64 Cell Line	embryonic stem cell
4	chr1:84542400-84543400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr1:84542400-84543400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:84542400-84544400	Active TSS	HMEC	breast
7	chr1:84542400-84544600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:84542400-84544600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr1:84542400-84544600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:84542400-84544600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
11	chr1:84542400-84544800	Active TSS	H1 Cell Line	embryonic stem cell
12	chr1:84542400-84544800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:84542400-84544800	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:84542400-84544800	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr1:84542400-84545000	Active TSS	H9 Cell Line	embryonic stem cell
16	chr1:84542400-84545000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr1:84542600-84543400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:84542600-84544200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:84542600-84544400	Active TSS	Brain Anterior Caudate	brain
20	chr1:84542600-84544400	Active TSS	Fetal Muscle Leg	muscle
21	chr1:84542600-84544400	Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr1:84542600-84544400	Active TSS	K562	blood
23	chr1:84542600-84544400	Active TSS	Osteobl	bone
24	chr1:84542600-84544800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr1:84542600-84544800	Active TSS	A549	lung
26	chr1:84542600-84545000	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr1:84542600-84545000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
28	chr1:84542600-84545000	Active TSS	Brain Cingulate Gyrus	brain
29	chr1:84542600-84545000	Active TSS	NHLF	lung
30	chr1:84542800-84543400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr1:84542800-84543400	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
32	chr1:84542800-84543800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr1:84542800-84544200	Active TSS	Brain Germinal Matrix	brain
34	chr1:84542800-84544200	Active TSS	Fetal Thymus	thymus
35	chr1:84542800-84544200	Active TSS	Rectal Mucosa Donor 31	rectum
36	chr1:84542800-84544200	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr1:84542800-84544200	Active TSS	Stomach Smooth Muscle	stomach
38	chr1:84542800-84544400	Active TSS	Fetal Intestine Small	intestine
39	chr1:84542800-84544400	Active TSS	Right Ventricle	heart
40	chr1:84542800-84544600	Active TSS	Colon Smooth Muscle	Colon
41	chr1:84542800-84544600	Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr1:84542800-84544600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr1:84542800-84544600	Active TSS	Hela-S3	cervix
44	chr1:84542800-84544800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr1:84542800-84544800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr1:84542800-84544800	Active TSS	Pancreatic Islets	Pancreatic Islet
47	chr1:84542800-84544800	Active TSS	Fetal Muscle Trunk	muscle
48	chr1:84542800-84544800	Active TSS	NHDF-Ad	bronchial
49	chr1:84542800-84545000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr1:84542800-84545000	Active TSS	iPS-15b Cell Line	embryonic stem cell

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