Variant report

Variant	rs2817213
Chromosome Location	chr6:24496054-24496055
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	ELF1	chr6:24494672-24496093	GM12878	blood:	n/a	chr6:24495026-24495038
2	MTA3	chr6:24494777-24496155	GM12878	blood:	n/a	n/a
3	SIN3A	chr6:24494694-24496103	H1-hESC	embryonic stem cell:	n/a	n/a
4	MAX	chr6:24495614-24496192	MCF-7	breast:	n/a	chr6:24495932-24495942
5	CBX3	chr6:24494815-24496262	K562	blood:	n/a	n/a
6	MAX	chr6:24495719-24496151	H1-hESC	embryonic stem cell:	n/a	chr6:24495932-24495942
7	USF1	chr6:24495736-24496068	ECC-1	luminal epithelium:	n/a	n/a
8	MYC	chr6:24494790-24496136	K562	blood:	n/a	chr6:24495932-24495942
9	MXI1	chr6:24495782-24496070	K562	blood:	n/a	n/a
10	MAX	chr6:24494798-24496214	ECC-1	luminal epithelium:	n/a	chr6:24495932-24495942
11	POLR2A	chr6:24494910-24496072	NB4	blood:	n/a	n/a
12	CTCF	chr6:24494347-24496072	SK-N-SH	brain:	n/a	n/a
13	MAX	chr6:24494838-24496188	A549	lung:	n/a	chr6:24495932-24495942
14	E2F6	chr6:24494853-24496071	H1-hESC	embryonic stem cell:	n/a	chr6:24495032-24495041
15	BCLAF1	chr6:24494844-24496229	GM12878	blood:	n/a	chr6:24495035-24495044 chr6:24495925-24495934
16	HEY1	chr6:24494876-24496060	HepG2	liver:	n/a	n/a
17	RCOR1	chr6:24494549-24496168	K562	blood:	n/a	n/a
18	MYC	chr6:24494869-24496129	K562	blood:	n/a	chr6:24495932-24495942
19	POLR2A	chr6:24494732-24496094	GM19193	blood:	n/a	n/a
20	MAX	chr6:24494825-24496208	ECC-1	luminal epithelium:	n/a	chr6:24495932-24495942
21	MYC	chr6:24494913-24496134	HepG2	liver:	n/a	chr6:24495932-24495942
22	USF1	chr6:24495718-24496070	H1-hESC	embryonic stem cell:	n/a	n/a
23	POLR2A	chr6:24494608-24496269	HepG2	liver:	n/a	n/a
24	POLR2A	chr6:24494793-24496127	HepG2	liver:	n/a	n/a
25	ZBTB7A	chr6:24494859-24496079	ECC-1	luminal epithelium:	n/a	chr6:24495066-24495075 chr6:24495157-24495166
26	MAX	chr6:24494649-24496188	A549	lung:	n/a	chr6:24495932-24495942
27	FOXA1	chr6:24495719-24496068	HepG2	liver:	n/a	n/a
28	MAZ	chr6:24494922-24496065	HepG2	liver:	n/a	n/a
29	USF1	chr6:24495724-24496075	H1-hESC	embryonic stem cell:	n/a	n/a
30	BHLHE40	chr6:24494774-24496091	HepG2	liver:	n/a	n/a
31	MAX	chr6:24494799-24496122	H1-hESC	embryonic stem cell:	n/a	chr6:24495932-24495942
32	MAX	chr6:24494592-24496234	HepG2	liver:	n/a	chr6:24495932-24495942
33	POLR2A	chr6:24494797-24496054	H1-neurons	neurons:	n/a	n/a
34	E2F6	chr6:24494761-24496123	K562	blood:	n/a	chr6:24495032-24495041
35	MAX	chr6:24494891-24496140	NB4	blood:	n/a	chr6:24495932-24495942
36	MYC	chr6:24495463-24496068	H1-hESC	embryonic stem cell:	n/a	chr6:24495932-24495942
37	MAX	chr6:24494835-24496201	K562	blood:	n/a	chr6:24495932-24495942
38	RELA	chr6:24494974-24496102	GM15510	blood:	n/a	n/a
39	TBL1XR1	chr6:24495671-24496106	GM12878	blood:	n/a	n/a
40	POLR2A	chr6:24494831-24496098	Raji	blood:	n/a	n/a
41	RUNX3	chr6:24494838-24496059	GM12878	blood:	n/a	n/a
42	CTBP2	chr6:24494773-24496059	H1-hESC	embryonic stem cell:	n/a	n/a
43	MAX	chr6:24494839-24496097	GM12878	blood:	n/a	chr6:24495932-24495942
44	MAZ	chr6:24495038-24496089	GM12878	blood:	n/a	n/a
45	POLR2A	chr6:24494775-24496102	H1-hESC	embryonic stem cell:	n/a	n/a
46	MAX	chr6:24494765-24496183	MCF-7	breast:	n/a	chr6:24495932-24495942
47	FOXA1	chr6:24495569-24496097	HepG2	liver:	n/a	n/a
48	SIN3AK20	chr6:24495723-24496063	HepG2	liver:	n/a	n/a
49	E2F6	chr6:24494717-24496229	H1-hESC	embryonic stem cell:	n/a	chr6:24495032-24495041
50	POLR2A	chr6:24494900-24496054	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:24473016..24474847-chr6:24495882..24498664,2	K562	blood:
2	chr6:24493014..24496474-chr6:24718971..24722650,4	K562	blood:
3	chr6:24493803..24496211-chr6:24773975..24776646,3	K562	blood:
4	chr6:24495510..24496378-chr6:24695478..24696466,2	MCF-7	breast:
5	chr6:24487824..24490266-chr6:24492770..24497111,3	MCF-7	breast:
6	chr6:24431084..24431585-chr6:24495592..24496144,2	MCF-7	breast:
7	chr6:24494650..24496587-chr6:24665440..24668079,2	MCF-7	breast:
8	chr6:24402909..24405943-chr6:24492830..24496087,3	K562	blood:
9	chr6:24488265..24492557-chr6:24493494..24498787,7	K562	blood:
10	chr6:24401784..24404907-chr6:24494976..24497958,4	MCF-7	breast:
11	chr6:24494081..24496615-chr6:24665704..24668263,2	K562	blood:
12	chr6:24494955..24497307-chr6:24719219..24721474,2	MCF-7	breast:
13	chr6:24483355..24485478-chr6:24495554..24497195,2	MCF-7	breast:
14	chr6:24495596..24498223-chr6:24565020..24567302,2	MCF-7	breast:
15	chr6:24495638..24500234-chr6:24504925..24509115,5	K562	blood:

Variant related genes	Relation type
GPLD1	TF binding region
ENSG00000112308	Chromatin interaction
ENSG00000112304	Chromatin interaction
ENSG00000111802	Chromatin interaction
ENSG00000112293	Chromatin interaction
ENSG00000112312	Chromatin interaction
ENSG00000124532	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1126617	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12190732	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12190926	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12197859	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs13193549	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs1883415	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2076316	0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2076317	0.90[ASN][1000 genomes]
rs2244216	0.81[AMR][1000 genomes]
rs2245668	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2245674	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2744567	0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2744568	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2744575	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2744577	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2744578	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2744579	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2760118	0.85[ASN][1000 genomes]
rs2760126	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760129	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2760131	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2760132	0.94[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2760140	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2760141	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2760144	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2760154	0.80[ASN][1000 genomes]
rs2817207	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2817211	0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2817216	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2817246	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2817257	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4646830	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs760903	0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7775073	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7775307	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2817213	ALDH5A1	cis	Heart Left Ventricle	GTEx
rs2817213	ALDH5A1	cis	Thyroid	GTEx
rs2817213	ALDH5A1	cis	lung	GTEx
rs2817213	ALDH5A1	Cis_1M	lymphoblastoid	RTeQTL
rs2817213	MRS2L	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:24494400-24496200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:24494400-24496200	Active TSS	H9 Cell Line	embryonic stem cell
3	chr6:24494400-24496200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr6:24494400-24496200	Active TSS	Aorta	Aorta
5	chr6:24494400-24496200	Active TSS	Fetal Kidney	kidney
6	chr6:24494400-24496200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr6:24494600-24496200	Active TSS	Ovary	ovary
8	chr6:24494600-24496200	Active TSS	Pancreas	Pancrea
9	chr6:24494600-24496200	Active TSS	HSMMtube	muscle
10	chr6:24494800-24496200	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr6:24494800-24496200	Active TSS	Brain Anterior Caudate	brain
12	chr6:24494800-24496200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
13	chr6:24494800-24496200	Active TSS	Colon Smooth Muscle	Colon
14	chr6:24494800-24496200	Active TSS	Left Ventricle	heart
15	chr6:24494800-24496200	Active TSS	Right Ventricle	heart
16	chr6:24494800-24496400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:24494800-24496600	Active TSS	Brain Cingulate Gyrus	brain
18	chr6:24495000-24496200	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr6:24495000-24496200	Active TSS	iPS-15b Cell Line	embryonic stem cell
20	chr6:24495000-24496200	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr6:24495000-24496200	Active TSS	Fetal Lung	lung
22	chr6:24495000-24496400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr6:24495200-24496200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
24	chr6:24495200-24496200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr6:24495400-24496200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
26	chr6:24495400-24496200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
27	chr6:24495400-24496600	Flanking Active TSS	Primary hematopoietic stem cells	blood
28	chr6:24495400-24496600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr6:24495600-24496200	Flanking Active TSS	Primary B cells from cord blood	blood
30	chr6:24495600-24496200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr6:24495600-24496200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
32	chr6:24495600-24496200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:24495600-24496200	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr6:24495600-24496200	Flanking Active TSS	Fetal Muscle Leg	muscle
35	chr6:24495600-24496200	Flanking Active TSS	Fetal Stomach	stomach
36	chr6:24495600-24496200	Flanking Active TSS	Fetal Thymus	thymus
37	chr6:24495600-24496200	Active TSS	Right Atrium	heart
38	chr6:24495600-24496200	Flanking Active TSS	GM12878-XiMat	blood
39	chr6:24495600-24496400	Flanking Active TSS	Adipose Nuclei	Adipose
40	chr6:24495600-24496600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr6:24495600-24496600	Flanking Active TSS	Dnd41	blood
42	chr6:24495800-24496200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
43	chr6:24495800-24496200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr6:24495800-24496200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr6:24495800-24496200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
46	chr6:24495800-24496200	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr6:24495800-24496200	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr6:24495800-24496200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
49	chr6:24495800-24496200	Flanking Active TSS	Fetal Intestine Small	intestine
50	chr6:24495800-24496200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links