Variant report

Variant	rs6576959
Chromosome Location	chr1:84543546-84543547
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	GABPA	chr1:84543345-84543778	HepG2	liver:	n/a	n/a
2	CCNT2	chr1:84543165-84544195	K562	blood:	n/a	chr1:84543960-84543969
3	GABPA	chr1:84543042-84543882	SK-N-SH	brain:	n/a	n/a
4	TAF1	chr1:84543182-84543673	A549	lung:	n/a	n/a
5	ETS1	chr1:84543144-84543619	K562	blood:	n/a	chr1:84543482-84543495 chr1:84543601-84543612
6	TCF12	chr1:84543345-84544168	ECC-1	luminal epithelium:	n/a	chr1:84543587-84543594
7	HEY1	chr1:84543060-84543700	K562	blood:	n/a	chr1:84543529-84543544 chr1:84543640-84543655
8	POLR2A	chr1:84543032-84543968	HCT-116	colon:	n/a	n/a
9	EGR1	chr1:84543405-84543762	GM12878	blood:	n/a	chr1:84543643-84543652 chr1:84543536-84543550 chr1:84543635-84543644 chr1:84543603-84543617
10	EGR1	chr1:84543352-84543753	K562	blood:	n/a	chr1:84543643-84543652 chr1:84543536-84543550 chr1:84543635-84543644 chr1:84543603-84543617
11	ATF3	chr1:84543471-84543757	K562	blood:	n/a	chr1:84543641-84543650 chr1:84543645-84543654 chr1:84543690-84543699 chr1:84543605-84543614 chr1:84543554-84543574
12	POLR2A	chr1:84543051-84544048	ECC-1	luminal epithelium:	n/a	n/a
13	MAX	chr1:84542943-84543742	SK-N-SH	brain:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
14	POLR2A	chr1:84543024-84544026	GM12891	blood:	n/a	n/a
15	RAD21	chr1:84543103-84543565	Hela-S3	cervix:	n/a	n/a
16	GABPA	chr1:84543094-84544099	K562	blood:	n/a	n/a
17	POLR2A	chr1:84542986-84544447	Hela-S3	cervix:	n/a	n/a
18	BCLAF1	chr1:84543128-84543608	GM12878	blood:	n/a	chr1:84543570-84543579
19	ZBTB7A	chr1:84543430-84543799	HepG2	liver:	n/a	n/a
20	POLR2A	chr1:84543250-84543923	HUVEC	blood vessel:	n/a	n/a
21	HEY1	chr1:84543045-84543875	HepG2	liver:	n/a	chr1:84543529-84543544 chr1:84543640-84543655
22	POLR2A	chr1:84543236-84543756	SK-N-MC	brain:	n/a	n/a
23	CHD2	chr1:84543339-84543660	H1-hESC	embryonic stem cell:	n/a	n/a
24	YY1	chr1:84543286-84543959	K562	blood:	n/a	n/a
25	MAX	chr1:84543002-84544430	K562	blood:	n/a	chr1:84543151-84543161 chr1:84543360-84543369 chr1:84544133-84544143
26	TCF3	chr1:84543285-84543702	GM12878	blood:	n/a	n/a
27	BACH1	chr1:84543125-84543656	H1-hESC	embryonic stem cell:	n/a	n/a
28	POLR2A	chr1:84543116-84543863	K562	blood:	n/a	n/a
29	POLR2A	chr1:84543254-84544272	HepG2	liver:	n/a	n/a
30	MYC	chr1:84543092-84543631	HepG2	liver:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
31	POLR2A	chr1:84543085-84543668	GM12891	blood:	n/a	n/a
32	TAF1	chr1:84543113-84543852	K562	blood:	n/a	n/a
33	MAX	chr1:84542945-84544346	NB4	blood:	n/a	chr1:84543151-84543161 chr1:84543360-84543369 chr1:84544133-84544143
34	ZNF384	chr1:84543279-84543565	K562	blood:	n/a	n/a
35	TAF1	chr1:84543367-84543560	GM12891	blood:	n/a	n/a
36	POLR2A	chr1:84543216-84543860	HepG2	liver:	n/a	n/a
37	TCF7L2	chr1:84543219-84543751	PANC-1	pancreas:	n/a	n/a
38	GTF2F1	chr1:84543035-84543694	K562	blood:	n/a	n/a
39	MYC	chr1:84542974-84543827	MCF10A-Er-Src	breast:	n/a	chr1:84543151-84543161 chr1:84543360-84543369
40	EGR1	chr1:84543335-84543821	ECC-1	luminal epithelium:	n/a	chr1:84543643-84543652 chr1:84543536-84543550 chr1:84543635-84543644 chr1:84543603-84543617
41	RAD21	chr1:84543056-84543546	IMR90	lung:	n/a	n/a
42	GABPA	chr1:84543274-84543757	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr1:84543116-84543603	GM12892	blood:	n/a	n/a
44	HCFC1	chr1:84542987-84543859	K562	blood:	n/a	n/a
45	POLR2A	chr1:84543146-84543988	HepG2	liver:	n/a	n/a
46	TAF1	chr1:84543478-84543785	SK-N-SH	brain:	n/a	n/a
47	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
48	ZBTB7A	chr1:84543051-84544273	ECC-1	luminal epithelium:	n/a	n/a
49	MXI1	chr1:84543005-84544827	IMR90	lung:	n/a	n/a
50	ARID3A	chr1:84543380-84543588	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:84543539-84543589	Caco-2	colon:	n/a
2	chr1:84543539-84543589	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:84543539-84543589	HCF	heart:	n/a
4	chr1:84543539-84543589	HCPEpiC	choroid plexus:	n/a
5	chr1:84543539-84543589	HRPEpiC	eye:	n/a
6	chr1:84543539-84543589	A549	lung:	n/a
7	chr1:84543539-84543589	HRCEpiC	kidney:	n/a
8	chr1:84543539-84543589	HMEC	breast:	n/a
9	chr1:84543539-84543589	T-47D	breast:	n/a
10	chr1:84543539-84543589	AG04450	lung:	fetal
11	chr1:84543539-84543589	HEEpiC	esophagus:	n/a
12	chr1:84543539-84543589	K562	blood:	n/a
13	chr1:84543539-84543589	HAEpiC	amniotic membrane:	n/a
14	chr1:84543539-84543589	BJ	skin:	n/a
15	chr1:84543539-84543589	ECC-1	luminal epithelium:	n/a
16	chr1:84543539-84543589	SKMC	muscle:	n/a
17	chr1:84543539-84543589	AG09319	gingival:	n/a
18	chr1:84543539-84543589	SK-N-SH	brain:	n/a
19	chr1:84543539-84543589	IMR90	lung:	fetal
20	chr1:84543539-84543589	GM12892	blood:	n/a
21	chr1:84543539-84543589	AG10803	skin:	n/a
22	chr1:84543539-84543589	NB4	blood:	n/a
23	chr1:84543539-84543589	SK-N-MC	brain:	n/a
24	chr1:84543539-84543589	H1-hESC	embryonic stem cell:	embryo
25	chr1:84543539-84543589	GM12878	blood:	n/a
26	chr1:84543539-84543589	Jurkat	blood:	n/a
27	chr1:84543539-84543589	GM19239	blood:	n/a
28	chr1:84543539-84543589	HCT-116	colon:	n/a
29	chr1:84543539-84543589	HNPCEpiC	eye:	n/a
30	chr1:84543539-84543589	PANC-1	pancreas:	n/a
31	chr1:84543539-84543589	U87	brain:	n/a
32	chr1:84543539-84543589	HCM	heart:	n/a
33	chr1:84543539-84543589	CMK	blood:	n/a
34	chr1:84543539-84543589	MCF10A-Er-Src	breast:	n/a
35	chr1:84543539-84543589	HUVEC	blood vessel:	n/a
36	chr1:84543539-84543589	SAEC	small airway:	n/a
37	chr1:84543539-84543589	BE2_C	brain:	n/a
38	chr1:84543539-84543589	PrEC	prostate:	n/a
39	chr1:84543539-84543589	HL-60	blood:	n/a
40	chr1:84543539-84543589	RPTEC	kidney:	n/a
41	chr1:84543539-84543589	AG09309	skin:	n/a
42	chr1:84543539-84543589	LNCaP	prostate:	n/a
43	chr1:84543539-84543589	GM06990	blood:	n/a
44	chr1:84543539-84543589	PFSK-1	brain:	n/a
45	chr1:84543539-84543589	NHBE	bronchial:	n/a
46	chr1:84543539-84543589	NH-A	brain:	n/a
47	chr1:84543539-84543589	AG04449	skin:	fetal
48	chr1:84543539-84543589	GM12891	blood:	n/a
49	chr1:84543539-84543589	Hela-S3	cervix:	n/a
50	chr1:84543539-84543589	SK-N-SH_RA	brain:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:84463410..84466364-chr1:84542152..84546505,5	K562	blood:
2	chr1:84543517..84544097-chr5:34915086..34915845,2	Hela-S3	cervix:
3	chr1:84543103..84544767-chr1:84969541..84972530,2	K562	blood:
4	chr1:84542242..84543745-chr1:85154770..85157524,2	K562	blood:
5	chr1:84542977..84543701-chr9:140135375..140136244,2	Hela-S3	cervix:
6	chr1:84543429..84544009-chr3:122233490..122234112,2	Hela-S3	cervix:
7	chr1:84541598..84548799-chr1:84549003..84554628,15	K562	blood:
8	chr1:84377090..84379247-chr1:84542414..84544902,2	K562	blood:
9	chr1:84543365..84543953-chr2:136633448..136634387,2	Hela-S3	cervix:

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

Variant related genes	Relation type
PRKACB	TF binding region
PRKACB	CpG island
ENSG00000188229	Chromatin interaction
ENSG00000122432	Chromatin interaction
ENSG00000114030	Chromatin interaction
ENSG00000137941	Chromatin interaction
ENSG00000113460	Chromatin interaction
ENSG00000174021	Chromatin interaction
ENSG00000076003	Chromatin interaction
ENSG00000117155	Chromatin interaction
ENSG00000213540	Chromatin interaction
ENSG00000113456	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1021491	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10874427	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1603000	0.91[EUR][1000 genomes]
rs2250806	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2642186	0.91[EUR][1000 genomes]
rs2792973	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2792975	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2792976	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs594631	0.85[EUR][1000 genomes]
rs599686	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs603939	0.88[EUR][1000 genomes]
rs617568	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs638545	0.85[EUR][1000 genomes]
rs648856	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs650629	0.85[EUR][1000 genomes]
rs652489	0.82[EUR][1000 genomes]
rs6701486	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[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	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	chr1:84542400-84544400	Active TSS	HMEC	breast
5	chr1:84542400-84544600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:84542400-84544600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:84542400-84544600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:84542400-84544600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:84542400-84544800	Active TSS	H1 Cell Line	embryonic stem cell
10	chr1:84542400-84544800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:84542400-84544800	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr1:84542400-84544800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr1:84542400-84545000	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:84542400-84545000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr1:84542600-84544200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr1:84542600-84544400	Active TSS	Brain Anterior Caudate	brain
17	chr1:84542600-84544400	Active TSS	Fetal Muscle Leg	muscle
18	chr1:84542600-84544400	Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr1:84542600-84544400	Active TSS	K562	blood
20	chr1:84542600-84544400	Active TSS	Osteobl	bone
21	chr1:84542600-84544800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:84542600-84544800	Active TSS	A549	lung
23	chr1:84542600-84545000	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr1:84542600-84545000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:84542600-84545000	Active TSS	Brain Cingulate Gyrus	brain
26	chr1:84542600-84545000	Active TSS	NHLF	lung
27	chr1:84542800-84543800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr1:84542800-84544200	Active TSS	Brain Germinal Matrix	brain
29	chr1:84542800-84544200	Active TSS	Fetal Thymus	thymus
30	chr1:84542800-84544200	Active TSS	Rectal Mucosa Donor 31	rectum
31	chr1:84542800-84544200	Active TSS	Skeletal Muscle Female	skeletal muscle
32	chr1:84542800-84544200	Active TSS	Stomach Smooth Muscle	stomach
33	chr1:84542800-84544400	Active TSS	Fetal Intestine Small	intestine
34	chr1:84542800-84544400	Active TSS	Right Ventricle	heart
35	chr1:84542800-84544600	Active TSS	Colon Smooth Muscle	Colon
36	chr1:84542800-84544600	Active TSS	Duodenum Smooth Muscle	Duodenum
37	chr1:84542800-84544600	Active TSS	Fetal Adrenal Gland	Adrenal Gland
38	chr1:84542800-84544600	Active TSS	Hela-S3	cervix
39	chr1:84542800-84544800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr1:84542800-84544800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr1:84542800-84544800	Active TSS	Pancreatic Islets	Pancreatic Islet
42	chr1:84542800-84544800	Active TSS	Fetal Muscle Trunk	muscle
43	chr1:84542800-84544800	Active TSS	NHDF-Ad	bronchial
44	chr1:84542800-84545000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr1:84542800-84545000	Active TSS	iPS-15b Cell Line	embryonic stem cell
46	chr1:84542800-84545000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:84542800-84545000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr1:84542800-84545000	Active TSS	Brain Angular Gyrus	brain
49	chr1:84542800-84545000	Active TSS	HSMMtube	muscle
50	chr1:84543000-84543600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood

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