Variant report

Variant	rs4646828
Chromosome Location	chr6:24494924-24494925
allele	C/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	ELF1	chr6:24494672-24496093	GM12878	blood:	n/a	chr6:24495026-24495038
2	NFIC	chr6:24494817-24495861	HepG2	liver:	n/a	n/a
3	TBP	chr6:24494843-24495984	H1-hESC	embryonic stem cell:	n/a	n/a
4	MTA3	chr6:24494777-24496155	GM12878	blood:	n/a	n/a
5	CTCF	chr6:24494798-24495327	MCF-7	breast:	n/a	n/a
6	POLR2A	chr6:24494911-24496047	HL-60	blood:	n/a	n/a
7	EBF1	chr6:24494866-24495971	GM12878	blood:	n/a	chr6:24495689-24495699 chr6:24495688-24495699
8	POLR2A	chr6:24494917-24496003	GM12878	blood:	n/a	n/a
9	YY1	chr6:24494905-24495569	K562	blood:	n/a	chr6:24495026-24495040 chr6:24495032-24495041
10	YY1	chr6:24494898-24495584	ECC-1	luminal epithelium:	n/a	chr6:24495026-24495040 chr6:24495032-24495041
11	SIN3A	chr6:24494694-24496103	H1-hESC	embryonic stem cell:	n/a	n/a
12	HNF4G	chr6:24494840-24495680	HepG2	liver:	n/a	chr6:24495016-24495029 chr6:24495016-24495028 chr6:24495018-24495040
13	ELF1	chr6:24494872-24495822	GM12878	blood:	n/a	chr6:24495026-24495038
14	CBX3	chr6:24494815-24496262	K562	blood:	n/a	n/a
15	YY1	chr6:24494900-24495599	SK-N-SH_RA	brain:	n/a	chr6:24495026-24495040 chr6:24495032-24495041
16	KAP1	chr6:24494836-24496050	HEK293	kidney:	n/a	chr6:24494996-24495004
17	POLR2A	chr6:24494908-24495337	HepG2	liver:	n/a	n/a
18	MYBL2	chr6:24494656-24495436	HepG2	liver:	n/a	n/a
19	MYC	chr6:24494790-24496136	K562	blood:	n/a	chr6:24495932-24495942
20	HDAC2	chr6:24494898-24495563	K562	blood:	n/a	chr6:24495176-24495185
21	EGR1	chr6:24494886-24495538	ECC-1	luminal epithelium:	n/a	chr6:24495177-24495186
22	CTCF	chr6:24494883-24495705	K562	blood:	n/a	n/a
23	MAX	chr6:24494749-24495449	MCF-7	breast:	n/a	n/a
24	CTCF	chr6:24494902-24495207	HepG2	liver:	n/a	n/a
25	CTCF	chr6:24494875-24495221	SK-N-SH_RA	brain:	n/a	n/a
26	HDAC2	chr6:24494761-24495161	H1-hESC	embryonic stem cell:	n/a	n/a
27	POLR2A	chr6:24494889-24495985	ECC-1	luminal epithelium:	n/a	n/a
28	SMARCB1	chr6:24494645-24496035	Hela-S3	cervix:	n/a	n/a
29	POLR2A	chr6:24494827-24496019	MCF-7	breast:	n/a	n/a
30	MAX	chr6:24494798-24496214	ECC-1	luminal epithelium:	n/a	chr6:24495932-24495942
31	POLR2A	chr6:24494910-24496072	NB4	blood:	n/a	n/a
32	CTCF	chr6:24494347-24496072	SK-N-SH	brain:	n/a	n/a
33	ZBTB7A	chr6:24494923-24495305	K562	blood:	n/a	chr6:24495066-24495075 chr6:24495157-24495166
34	CHD2	chr6:24494720-24495241	GM12878	blood:	n/a	n/a
35	TAF1	chr6:24494872-24495859	H1-hESC	embryonic stem cell:	n/a	n/a
36	PML	chr6:24494743-24495313	GM12878	blood:	n/a	chr6:24494996-24495004
37	MAX	chr6:24494838-24496188	A549	lung:	n/a	chr6:24495932-24495942
38	POLR2A	chr6:24494890-24494925	Gliobla	brain:	n/a	n/a
39	E2F6	chr6:24494853-24496071	H1-hESC	embryonic stem cell:	n/a	chr6:24495032-24495041
40	POLR2A	chr6:24494822-24495395	GM12878	blood:	n/a	n/a
41	EP300	chr6:24494900-24495456	HepG2	liver:	n/a	chr6:24495034-24495050
42	BCLAF1	chr6:24494844-24496229	GM12878	blood:	n/a	chr6:24495035-24495044 chr6:24495925-24495934
43	RCOR1	chr6:24494703-24495960	HepG2	liver:	n/a	n/a
44	HEY1	chr6:24494876-24496060	HepG2	liver:	n/a	n/a
45	TEAD4	chr6:24494607-24495256	H1-hESC	embryonic stem cell:	n/a	n/a
46	RCOR1	chr6:24494549-24496168	K562	blood:	n/a	n/a
47	CTCF	chr6:24494910-24495199	GM19240	blood:	n/a	n/a
48	RCOR1	chr6:24494737-24495201	K562	blood:	n/a	n/a
49	CTCF	chr6:24494912-24495294	Spleen_OC	spleen:	n/a	n/a
50	CTCF	chr6:24494924-24495251	GM12892	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
2	chr6:24493803..24496211-chr6:24773975..24776646,3	K562	blood:
3	chr6:24492199..24495699-chr6:24718792..24721987,5	K562	blood:
4	chr6:24489101..24491684-chr6:24493403..24495493,2	MCF-7	breast:
5	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:
6	chr6:24494650..24496587-chr6:24665440..24668079,2	MCF-7	breast:
7	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
8	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
9	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
10	chr6:24487096..24491354-chr6:24491448..24495730,8	K562	blood:

Variant related genes	Relation type
ALDH5A1	TF binding region
ENSG00000111802	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000124532	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112308	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10946703	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1111013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1111014	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11758106	0.82[EUR][1000 genomes]
rs11759284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12208521	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13218564	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1810473	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34052391	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34517349	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35864956	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4712825	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62400473	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62400494	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9461028	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[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	esv2763542	chr6:24445131-24520637	Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv519552	chr6:24451256-24524704	Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv883480	chr6:24481299-24507519	Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
4	esv34020	chr6:24481299-24606036	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	esv3351586	chr6:24494123-24497171	Bivalent/Poised TSS Enhancers Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4646828	ALDH5A1	cis	lung	GTEx
rs4646828	ALDH5A1	cis	Muscle Skeletal	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24493200-24495000	Flanking Active TSS	K562	blood
2	chr6:24494000-24495000	Flanking Active TSS	Primary T cells from cord blood	blood
3	chr6:24494000-24495000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr6:24494000-24496000	Active TSS	Brain Angular Gyrus	brain
5	chr6:24494000-24496000	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr6:24494200-24495000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
7	chr6:24494200-24495000	Flanking Active TSS	HepG2	liver
8	chr6:24494200-24495200	Flanking Active TSS	Adipose Nuclei	Adipose
9	chr6:24494400-24495000	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
10	chr6:24494400-24495000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr6:24494400-24495000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
12	chr6:24494400-24495000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr6:24494400-24495000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr6:24494400-24495000	Flanking Active TSS	Liver	Liver
15	chr6:24494400-24495000	Flanking Active TSS	Brain Germinal Matrix	brain
16	chr6:24494400-24495000	Flanking Active TSS	Fetal Thymus	thymus
17	chr6:24494400-24495000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
18	chr6:24494400-24495000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr6:24494400-24495000	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr6:24494400-24495000	Flanking Active TSS	Thymus	Thymus
21	chr6:24494400-24495000	Flanking Active TSS	Hela-S3	cervix
22	chr6:24494400-24495200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
23	chr6:24494400-24495200	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr6:24494400-24495200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr6:24494400-24495200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
26	chr6:24494400-24495600	Active TSS	Cortex derived primary cultured neurospheres	brain
27	chr6:24494400-24495800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
28	chr6:24494400-24496000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:24494400-24496000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr6:24494400-24496000	Active TSS	Brain Substantia Nigra	brain
31	chr6:24494400-24496000	Active TSS	Fetal Brain Female	brain
32	chr6:24494400-24496200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
33	chr6:24494400-24496200	Active TSS	H9 Cell Line	embryonic stem cell
34	chr6:24494400-24496200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
35	chr6:24494400-24496200	Active TSS	Aorta	Aorta
36	chr6:24494400-24496200	Active TSS	Fetal Kidney	kidney
37	chr6:24494400-24496200	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr6:24494600-24495000	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr6:24494600-24495000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
40	chr6:24494600-24495000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:24494600-24495000	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr6:24494600-24495000	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr6:24494600-24495000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
44	chr6:24494600-24495000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
45	chr6:24494600-24495000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr6:24494600-24495000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
47	chr6:24494600-24495000	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr6:24494600-24495000	Flanking Active TSS	Esophagus	oesophagus
49	chr6:24494600-24495000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
50	chr6:24494600-24495000	Flanking Active TSS	Fetal Intestine Large	intestine

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