Variant report

Variant	rs62488688
Chromosome Location	chr8:9912613-9912614
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	RCOR1	chr8:9911619-9913206	K562	blood:	n/a	n/a
2	TAF1	chr8:9911897-9912682	HepG2	liver:	n/a	n/a
3	TAF1	chr8:9911936-9912680	H1-neurons	neurons:	n/a	n/a
4	TAF1	chr8:9911945-9912711	ECC-1	luminal epithelium:	n/a	n/a
5	E2F6	chr8:9911909-9912808	A549	lung:	n/a	chr8:9912311-9912321 chr8:9912208-9912217 chr8:9912226-9912236 chr8:9912216-9912223 chr8:9912298-9912307
6	POLR2A	chr8:9911513-9912814	GM12878	blood:	n/a	n/a
7	POLR2A	chr8:9911540-9913034	ProgFib	skin:	n/a	n/a
8	TAF1	chr8:9912034-9912699	Hela-S3	cervix:	n/a	n/a
9	POLR2A	chr8:9911777-9913143	GM12892	blood:	n/a	n/a
10	EBF1	chr8:9911538-9913164	GM12878	blood:	n/a	chr8:9912724-9912734 chr8:9912122-9912133
11	ATF2	chr8:9912232-9913171	H1-hESC	embryonic stem cell:	n/a	n/a
12	POLR2A	chr8:9910959-9913289	GM12878	blood:	n/a	n/a
13	CHD2	chr8:9911537-9912618	GM12878	blood:	n/a	chr8:9912216-9912223
14	HMGN3	chr8:9912072-9912780	K562	blood:	n/a	chr8:9912680-9912689 chr8:9912677-9912686
15	TAF7	chr8:9911904-9912707	H1-hESC	embryonic stem cell:	n/a	n/a
16	CTCF	chr8:9912500-9912650	RPTEC	kidney:	n/a	n/a
17	TBP	chr8:9912036-9912641	K562	blood:	n/a	n/a
18	CTCF	chr8:9912500-9912650	GM12868	blood:	n/a	n/a
19	RELA	chr8:9912004-9912617	GM19099	blood:	n/a	n/a
20	POLR2A	chr8:9911477-9913171	Hela-S3	cervix:	n/a	n/a
21	MAX	chr8:9911923-9912675	MCF-7	breast:	n/a	n/a
22	YY1	chr8:9911501-9912631	HepG2	liver:	n/a	chr8:9912504-9912518
23	SMARCB1	chr8:9911510-9913114	Hela-S3	cervix:	n/a	chr8:9912679-9912688
24	E2F6	chr8:9911729-9912785	K562	blood:	n/a	chr8:9912311-9912321 chr8:9912208-9912217 chr8:9912226-9912236 chr8:9912216-9912223 chr8:9912298-9912307
25	MAZ	chr8:9911580-9913277	IMR90	lung:	n/a	n/a
26	POLR2A	chr8:9911166-9913142	HepG2	liver:	n/a	n/a
27	EBF1	chr8:9911887-9912845	GM12878	blood:	n/a	chr8:9912724-9912734 chr8:9912122-9912133
28	POLR2A	chr8:9911578-9913091	GM10847	blood:	n/a	n/a
29	POLR2A	chr8:9911924-9913214	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr8:9911137-9913188	MCF10A-Er-Src	breast:	n/a	n/a
31	BHLHE40	chr8:9912102-9912808	K562	blood:	n/a	chr8:9912727-9912743 chr8:9912550-9912566
32	GABPA	chr8:9912033-9912624	Hela-S3	cervix:	n/a	chr8:9912207-9912218 chr8:9912297-9912306 chr8:9912297-9912311 chr8:9912209-9912218 chr8:9912207-9912216 chr8:9912297-9912308 chr8:9912204-9912218 chr8:9912193-9912202 chr8:9912207-9912221 chr8:9912294-9912308
33	CHD1	chr8:9912392-9913260	H1-hESC	embryonic stem cell:	n/a	n/a
34	POLR2A	chr8:9911390-9913168	GM12892	blood:	n/a	n/a
35	CTBP2	chr8:9911596-9912629	H1-hESC	embryonic stem cell:	n/a	n/a
36	POLR2A	chr8:9910902-9913264	GM12891	blood:	n/a	n/a
37	REST	chr8:9912077-9912679	A549	lung:	n/a	chr8:9912516-9912529
38	POLR2A	chr8:9911942-9912647	HUVEC	blood vessel:	n/a	n/a
39	GABPA	chr8:9911926-9912633	H1-hESC	embryonic stem cell:	n/a	chr8:9912207-9912218 chr8:9912297-9912306 chr8:9912297-9912311 chr8:9912209-9912218 chr8:9912207-9912216 chr8:9912297-9912308 chr8:9912204-9912218 chr8:9912193-9912202 chr8:9912207-9912221 chr8:9912294-9912308
40	TAF1	chr8:9911955-9913144	H1-hESC	embryonic stem cell:	n/a	n/a
41	HA-E2F1	chr8:9911573-9912638	Hela-S3	cervix:	n/a	chr8:9912311-9912321 chr8:9912208-9912217 chr8:9912226-9912236 chr8:9912216-9912223 chr8:9912298-9912307
42	YY1	chr8:9912085-9912674	K562	blood:	n/a	chr8:9912504-9912518
43	TBP	chr8:9912052-9913222	H1-hESC	embryonic stem cell:	n/a	n/a
44	E2F6	chr8:9911920-9912786	K562	blood:	n/a	chr8:9912311-9912321 chr8:9912208-9912217 chr8:9912226-9912236 chr8:9912216-9912223 chr8:9912298-9912307
45	MAX	chr8:9911484-9913104	GM12878	blood:	n/a	n/a
46	CTCF	chr8:9912500-9912650	SAEC	small airway:	n/a	n/a
47	CTCF	chr8:9912480-9912630	HBMEC	blood vessel:	n/a	n/a
48	NRF1	chr8:9911922-9912897	SK-N-SH	brain:	n/a	chr8:9912206-9912217 chr8:9912207-9912218 chr8:9912297-9912306 chr8:9912297-9912311 chr8:9912209-9912218 chr8:9912207-9912216 chr8:9912297-9912308 chr8:9912204-9912218 chr8:9912189-9912200 chr8:9912193-9912202 chr8:9912207-9912221 chr8:9912294-9912308
49	POLR2A	chr8:9911913-9913237	SK-N-MC	brain:	n/a	n/a
50	CTCF	chr8:9912440-9912710	GM12870	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:79825287..79825828-chr8:9912227..9912805,2	HCT-116	colon:
2	chr8:9912450..9914254-chr8:9914390..9916277,2	MCF-7	breast:
3	chr8:9912174..9913822-chr8:9921464..9923860,2	K562	blood:
4	chr12:53835095..53835707-chr8:9911850..9912740,2	Hela-S3	cervix:

Variant related genes	Relation type
ENSG00000260093	TF binding region
MSRA	TF binding region
ENSG00000197111	Chromatin interaction
ENSG00000205352	Chromatin interaction
ENSG00000262413	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs17150984	0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17150993	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2661754	0.89[ASN][1000 genomes]
rs2684000	0.91[AMR][1000 genomes]
rs62488680	0.91[AMR][1000 genomes]
rs62488687	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62488689	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62488690	0.89[ASN][1000 genomes]
rs62491204	0.91[AMR][1000 genomes]
rs6987910	0.88[AMR][1000 genomes];0.86[ASN][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	nsv530864	chr8:9097498-9914548	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv916493	chr8:9806580-10029482	Weak transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv869934	chr8:9806639-9940586	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv890343	chr8:9888729-9932797	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 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	chr8:9910800-9912800	Active TSS	Primary T regulatory cells fromperipheralblood	blood
2	chr8:9911000-9912800	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr8:9911000-9913200	Active TSS	HSMMtube	muscle
4	chr8:9911200-9912800	Active TSS	Colonic Mucosa	Colon
5	chr8:9911200-9912800	Active TSS	Skeletal Muscle Male	skeletal muscle
6	chr8:9911200-9913000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr8:9911200-9913000	Active TSS	Left Ventricle	heart
8	chr8:9911200-9913200	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr8:9911200-9913200	Active TSS	H1 Cell Line	embryonic stem cell
10	chr8:9911200-9913200	Active TSS	H9 Cell Line	embryonic stem cell
11	chr8:9911200-9913200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr8:9911200-9913200	Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr8:9911200-9913200	Active TSS	Aorta	Aorta
14	chr8:9911200-9913200	Active TSS	Psoas Muscle	Psoas
15	chr8:9911200-9913400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr8:9911200-9913400	Active TSS	Pancreatic Islets	Pancreatic Islet
17	chr8:9911400-9912800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr8:9911400-9912800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr8:9911400-9912800	Active TSS	Primary T cells from cord blood	blood
20	chr8:9911400-9912800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr8:9911400-9912800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr8:9911400-9912800	Active TSS	Brain Hippocampus Middle	brain
23	chr8:9911400-9912800	Active TSS	Esophagus	oesophagus
24	chr8:9911400-9912800	Active TSS	Fetal Heart	heart
25	chr8:9911400-9912800	Active TSS	Fetal Lung	lung
26	chr8:9911400-9912800	Active TSS	Fetal Stomach	stomach
27	chr8:9911400-9912800	Active TSS	Placenta Amnion	Placenta Amnion
28	chr8:9911400-9912800	Active TSS	Rectal Smooth Muscle	rectum
29	chr8:9911400-9912800	Bivalent/Poised TSS	HepG2	liver
30	chr8:9911400-9912800	Active TSS	NHLF	lung
31	chr8:9911400-9913000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr8:9911400-9913000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr8:9911400-9913000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr8:9911400-9913000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
35	chr8:9911400-9913000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
36	chr8:9911400-9913000	Active TSS	Gastric	stomach
37	chr8:9911400-9913000	Active TSS	NHDF-Ad	bronchial
38	chr8:9911400-9913200	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr8:9911400-9913200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr8:9911400-9913200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
41	chr8:9911400-9913200	Active TSS	Fetal Kidney	kidney
42	chr8:9911400-9913200	Active TSS	Lung	lung
43	chr8:9911400-9913200	Active TSS	Ovary	ovary
44	chr8:9911400-9913200	Active TSS	Pancreas	Pancrea
45	chr8:9911400-9913200	Active TSS	Right Ventricle	heart
46	chr8:9911400-9913200	Active TSS	Stomach Mucosa	stomach
47	chr8:9911400-9913400	Active TSS	Fetal Intestine Large	intestine
48	chr8:9911400-9913400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr8:9911600-9912800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr8:9911600-9912800	Active TSS	Liver	Liver

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