Variant report

Variant	rs2535246
Chromosome Location	chr6:29636409-29636410
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:61)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:29636366-29636416	ovcar-3	ovarian:	n/a
2	chr6:29636366-29636416	HUVEC	blood vessel:	n/a
3	chr6:29636366-29636416	AG04450	lung:	fetal
4	chr6:29636366-29636416	T-47D	breast:	n/a
5	chr6:29636366-29636416	AG10803	skin:	n/a
6	chr6:29636366-29636416	A549	lung:	n/a
7	chr6:29636366-29636416	HEEpiC	esophagus:	n/a
8	chr6:29636366-29636416	LNCaP	prostate:	n/a
9	chr6:29636366-29636416	MCF-7	breast:	n/a
10	chr6:29636366-29636416	Hela-S3	cervix:	n/a
11	chr6:29636366-29636416	GM12891	blood:	n/a
12	chr6:29636366-29636416	NB4	blood:	n/a
13	chr6:29636366-29636416	AG09319	gingival:	n/a
14	chr6:29636366-29636416	HCM	heart:	n/a
15	chr6:29636366-29636416	HCF	heart:	n/a
16	chr6:29636366-29636416	GM19239	blood:	n/a
17	chr6:29636366-29636416	NHBE	bronchial:	n/a
18	chr6:29636366-29636416	ProgFib	skin:	n/a
19	chr6:29636366-29636416	HRPEpiC	eye:	n/a
20	chr6:29636366-29636416	HCT-116	colon:	n/a
21	chr6:29636366-29636416	PFSK-1	brain:	n/a
22	chr6:29636366-29636416	NHDF-neo	bronchial:	n/a
23	chr6:29636366-29636416	SK-N-MC	brain:	n/a
24	chr6:29636366-29636416	HIPEpiC	eye:	n/a
25	chr6:29636366-29636416	RPTEC	kidney:	n/a
26	chr6:29636366-29636416	NT2-D1	testis:	n/a
27	chr6:29636366-29636416	HL-60	blood:	n/a
28	chr6:29636366-29636416	SK-N-SH	brain:	n/a
29	chr6:29636366-29636416	HAEpiC	amniotic membrane:	n/a
30	chr6:29636366-29636416	HCPEpiC	choroid plexus:	n/a
31	chr6:29636366-29636416	BJ	skin:	n/a
32	chr6:29636366-29636416	AG04449	skin:	fetal
33	chr6:29636366-29636416	HRCEpiC	kidney:	n/a
34	chr6:29636366-29636416	HepG2	liver:	n/a
35	chr6:29636366-29636416	SAEC	small airway:	n/a
36	chr6:29636366-29636416	HEK293	kidney:	embryo
37	chr6:29636366-29636416	ECC-1	luminal epithelium:	n/a
38	chr6:29636366-29636416	SK-N-SH_RA	brain:	n/a
39	chr6:29636366-29636416	Caco-2	colon:	n/a
40	chr6:29636366-29636416	SKMC	muscle:	n/a
41	chr6:29636366-29636416	HPAEpiC	pulmonary alveolar:	n/a
42	chr6:29636366-29636416	GM12878	blood:	n/a
43	chr6:29636366-29636416	GM12892	blood:	n/a
44	chr6:29636366-29636416	GM06990	blood:	n/a
45	chr6:29636366-29636416	HMEC	breast:	n/a
46	chr6:29636366-29636416	IMR90	lung:	fetal
47	chr6:29636366-29636416	Jurkat	blood:	n/a
48	chr6:29636366-29636416	AoSMC	blood vessel:	n/a
49	chr6:29636366-29636416	Hepatocyte	liver:	n/a
50	chr6:29636366-29636416	U87	brain:	n/a

(count:1 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29634001..29636635-chr6:29639490..29642126,2	K562	blood:

No data

Variant related genes	Relation type
MOG	CpG island

Extended variants
information (count: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1122947	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1984840	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079898	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2262263	0.81[ASN][1000 genomes]
rs2517913	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2535245	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2535260	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2735063	0.87[EUR][1000 genomes]
rs2747425	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2747453	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2747455	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs29231	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs29273	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2982837	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3095287	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129041	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3129074	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129087	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3129090	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131879	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131881	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3131882	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6456993	0.89[EUR][1000 genomes]
rs6941117	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7738159	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7774576	0.81[ASN][1000 genomes]
rs7776296	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9257931	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9258093	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258094	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258102	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258106	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9258111	0.81[ASN][1000 genomes]
rs9258114	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9258126	0.87[EUR][1000 genomes]
rs9258127	0.87[EUR][1000 genomes]
rs9258131	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2535246	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs2535246	HIST1H2BE	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29625000-29663600	Weak transcription	Right Atrium	heart
2	chr6:29630800-29643200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:29631400-29640200	Weak transcription	NHEK	skin
4	chr6:29632000-29638600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:29633600-29636600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr6:29633800-29636600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr6:29634600-29641000	Weak transcription	Brain Anterior Caudate	brain
8	chr6:29634600-29642000	Weak transcription	Brain Angular Gyrus	brain
9	chr6:29635200-29636600	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr6:29635600-29636600	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr6:29635600-29636600	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
12	chr6:29635600-29639600	Strong transcription	Brain Substantia Nigra	brain
13	chr6:29635800-29636600	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr6:29635800-29636600	Strong transcription	Brain Hippocampus Middle	brain
15	chr6:29636000-29636600	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr6:29636000-29639800	Strong transcription	Brain Cingulate Gyrus	brain
17	chr6:29636200-29636600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr6:29636400-29636600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
19	chr6:29636400-29637000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr6:29636400-29639000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:29636400-29643800	Weak transcription	Fetal Heart	heart

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