Variant report

Variant	rs6472219
Chromosome Location	chr8:66556722-66556723
allele	A/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	POLR2A	chr8:66556448-66557201	SK-N-MC	brain:	n/a	n/a
2	TEAD4	chr8:66555887-66557150	K562	blood:	n/a	n/a
3	POLR2A	chr8:66555772-66557688	HepG2	liver:	n/a	n/a
4	NFYA	chr8:66556722-66557020	GM12878	blood:	n/a	chr8:66556939-66556952
5	POLR2A	chr8:66555886-66557661	K562	blood:	n/a	n/a
6	POLR2A	chr8:66556626-66557171	GM12891	blood:	n/a	n/a
7	MAX	chr8:66556168-66557594	Hela-S3	cervix:	n/a	chr8:66556410-66556421 chr8:66556410-66556421 chr8:66556411-66556420 chr8:66556411-66556421
8	ZNF143	chr8:66556574-66557577	Hela-S3	cervix:	n/a	chr8:66557477-66557495 chr8:66557363-66557373
9	RFX5	chr8:66556693-66557478	GM12878	blood:	n/a	n/a
10	HEY1	chr8:66556538-66557235	K562	blood:	n/a	chr8:66557000-66557015 chr8:66557184-66557199
11	POLR2A	chr8:66556462-66557642	H1-neurons	neurons:	n/a	n/a
12	RFX5	chr8:66556385-66557664	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr8:66556432-66557705	HUVEC	blood vessel:	n/a	n/a
14	REST	chr8:66556020-66557897	H1-neurons	neurons:	n/a	chr8:66556783-66556796 chr8:66556824-66556834
15	ARID3A	chr8:66555657-66557626	K562	blood:	n/a	n/a
16	SP1	chr8:66556026-66557618	A549	lung:	n/a	chr8:66557320-66557332 chr8:66556925-66556934 chr8:66557320-66557332 chr8:66556926-66556935 chr8:66556221-66556242 chr8:66556926-66556935 chr8:66557322-66557331 chr8:66557315-66557329
17	E2F6	chr8:66555743-66557566	K562	blood:	n/a	chr8:66556797-66556806 chr8:66556222-66556231 chr8:66557364-66557373 chr8:66556395-66556404
18	TCF12	chr8:66556237-66557716	A549	lung:	n/a	chr8:66557314-66557324
19	IRF1	chr8:66555689-66557675	K562	blood:	n/a	chr8:66557542-66557554 chr8:66556222-66556231
20	POLR2A	chr8:66555705-66557694	K562	blood:	n/a	n/a
21	POLR2A	chr8:66556677-66557650	IMR90	lung:	n/a	n/a
22	POLR2A	chr8:66556559-66557598	A549	lung:	n/a	n/a
23	RELA	chr8:66556436-66557578	GM15510	blood:	n/a	n/a
24	POLR2A	chr8:66556036-66557659	GM12878	blood:	n/a	n/a
25	POLR2A	chr8:66555765-66557751	PBDE	blood:	n/a	n/a
26	POLR2A	chr8:66556191-66557746	HUVEC	blood vessel:	n/a	n/a
27	PAX5	chr8:66556619-66557638	GM12878	blood:	n/a	chr8:66556797-66556806
28	SIN3AK20	chr8:66556019-66557164	K562	blood:	n/a	n/a
29	STAT1	chr8:66556541-66557434	GM12878	blood:	n/a	n/a
30	SIN3AK20	chr8:66556379-66557774	PANC-1	pancreas:	n/a	n/a
31	PBX3	chr8:66556650-66557627	A549	lung:	n/a	chr8:66556941-66556950
32	FOXP2	chr8:66556483-66557260	SK-N-MC	brain:	n/a	n/a
33	BHLHE40	chr8:66556151-66557702	HepG2	liver:	n/a	chr8:66556411-66556420 chr8:66556412-66556421 chr8:66556411-66556420
34	POLR2A	chr8:66555821-66557647	K562	blood:	n/a	n/a
35	TAF1	chr8:66556564-66557125	PFSK-1	brain:	n/a	n/a
36	PBX3	chr8:66556651-66557104	GM12878	blood:	n/a	chr8:66556941-66556950
37	RCOR1	chr8:66556569-66557721	HepG2	liver:	n/a	n/a
38	POLR2A	chr8:66556612-66557680	GM19099	blood:	n/a	n/a
39	HEY1	chr8:66556377-66557687	K562	blood:	n/a	chr8:66556411-66556420 chr8:66557000-66557015 chr8:66557184-66557199
40	POLR2A	chr8:66556556-66557720	GM12892	blood:	n/a	n/a
41	MYC	chr8:66556154-66557081	MCF10A-Er-Src	breast:	n/a	chr8:66556410-66556421 chr8:66556410-66556421 chr8:66556411-66556420 chr8:66556411-66556421
42	CHD2	chr8:66556715-66557011	H1-hESC	embryonic stem cell:	n/a	n/a
43	POLR2A	chr8:66556484-66557272	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr8:66555742-66557603	K562	blood:	n/a	chr8:66556410-66556421 chr8:66556410-66556421 chr8:66556411-66556420 chr8:66556411-66556421
45	POLR2A	chr8:66556628-66557578	GM12878	blood:	n/a	n/a
46	PBX3	chr8:66556706-66557187	A549	lung:	n/a	chr8:66556941-66556950
47	CTCF	chr8:66555564-66557953	A549	lung:	n/a	chr8:66557373-66557386 chr8:66557371-66557387 chr8:66556142-66556151 chr8:66557370-66557388
48	RUNX3	chr8:66556620-66557680	GM12878	blood:	n/a	n/a
49	MYC	chr8:66556686-66557122	MCF-7	breast:	n/a	n/a
50	POLR2A	chr8:66556588-66557177	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr8:66540570..66542467-chr8:66555055..66556755,2	MCF-7	breast:
2	chr8:66544310..66548208-chr8:66554670..66559350,8	MCF-7	breast:
3	chr8:66543941..66549000-chr8:66554498..66559366,10	MCF-7	breast:
4	chr8:66555236..66558809-chr8:66619620..66621771,3	K562	blood:
5	chr8:66555940..66558809-chr8:66619620..66621771,2	K562	blood:

Variant related genes	Relation type
MTFR1	TF binding region
ENSG00000066855	Chromatin interaction
ENSG00000104442	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10091345	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10106749	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs10111844	0.87[EUR][1000 genomes]
rs10957358	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs10957359	0.85[EUR][1000 genomes]
rs13251307	0.96[CEU][hapmap]
rs13274205	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs13275168	0.96[CEU][hapmap];0.83[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13280521	0.92[CEU][hapmap]
rs13281090	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs13281981	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17395275	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs17396080	0.92[CEU][hapmap]
rs2357475	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34496943	0.87[EUR][1000 genomes]
rs35411381	0.85[EUR][1000 genomes]
rs4424306	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62507608	0.87[EUR][1000 genomes]
rs7007473	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7007987	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs7462352	0.84[EUR][1000 genomes]
rs7818909	0.93[CEU][hapmap]
rs7822627	0.85[EUR][1000 genomes]
rs7822707	0.93[CEU][hapmap]
rs7829434	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs869151	0.92[CEU][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761434	chr8:65578467-66567678	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs6472219	CTD-3025N20.3	cis	Esophagus Muscularis	GTEx
rs6472219	CTD-3025N20.3	cis	Artery Tibial	GTEx
rs6472219	CTD-3025N20.3	cis	Thyroid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:66555400-66556800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr8:66555400-66558200	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr8:66555400-66558600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr8:66555600-66556800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr8:66555600-66556800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr8:66555600-66556800	Flanking Active TSS	Adipose Nuclei	Adipose
7	chr8:66555600-66556800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr8:66555600-66556800	Flanking Active TSS	Hela-S3	cervix
9	chr8:66555600-66556800	Flanking Active TSS	HMEC	breast
10	chr8:66555600-66556800	Flanking Active TSS	NHEK	skin
11	chr8:66555600-66556800	Flanking Active TSS	Osteobl	bone
12	chr8:66555600-66557800	Active TSS	Colonic Mucosa	Colon
13	chr8:66555600-66557800	Active TSS	Fetal Intestine Large	intestine
14	chr8:66555600-66557800	Active TSS	Fetal Intestine Small	intestine
15	chr8:66555600-66557800	Active TSS	Psoas Muscle	Psoas
16	chr8:66555600-66558000	Active TSS	HUES48 Cell Line	embryonic stem cell
17	chr8:66555600-66558000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr8:66555600-66558000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr8:66555600-66558000	Active TSS	Colon Smooth Muscle	Colon
20	chr8:66555600-66558000	Active TSS	Fetal Lung	lung
21	chr8:66555600-66558200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr8:66555800-66556800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr8:66555800-66556800	Flanking Active TSS	Primary hematopoietic stem cells	blood
24	chr8:66555800-66556800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
25	chr8:66555800-66556800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
26	chr8:66555800-66556800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr8:66555800-66556800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr8:66555800-66556800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
29	chr8:66555800-66556800	Flanking Active TSS	Liver	Liver
30	chr8:66555800-66556800	Flanking Active TSS	Dnd41	blood
31	chr8:66555800-66556800	Flanking Active TSS	NH-A	brain
32	chr8:66555800-66557200	Active TSS	Right Atrium	heart
33	chr8:66555800-66557200	Bivalent/Poised TSS	HepG2	liver
34	chr8:66555800-66557600	Active TSS	Fetal Heart	heart
35	chr8:66555800-66557600	Active TSS	Fetal Muscle Trunk	muscle
36	chr8:66555800-66557800	Active TSS	Pancreas	Pancrea
37	chr8:66555800-66558000	Active TSS	H9 Cell Line	embryonic stem cell
38	chr8:66555800-66558000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr8:66555800-66558000	Active TSS	Aorta	Aorta
40	chr8:66555800-66558200	Active TSS	H1 Cell Line	embryonic stem cell
41	chr8:66555800-66558200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr8:66555800-66558200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr8:66555800-66558200	Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr8:66555800-66558200	Active TSS	Right Ventricle	heart
45	chr8:66555800-66558200	Active TSS	NHDF-Ad	bronchial
46	chr8:66556000-66556800	Flanking Active TSS	Primary B cells from peripheral blood	blood
47	chr8:66556000-66556800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr8:66556000-66556800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
49	chr8:66556000-66556800	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr8:66556000-66556800	Flanking Active TSS	Stomach Smooth Muscle	stomach

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