Variant report

Variant	rs2523864
Chromosome Location	chr6:31018546-31018547
allele	A/G
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:3)
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	chr6:31018523-31018573	RPTEC	kidney:	n/a
2	chr6:31018523-31018573	AG09319	gingival:	n/a
3	chr6:31018523-31018573	HCM	heart:	n/a
4	chr6:31018523-31018573	NHBE	bronchial:	n/a
5	chr6:31018523-31018573	HEK293	kidney:	embryo
6	chr6:31018523-31018573	LNCaP	prostate:	n/a
7	chr6:31018523-31018573	MCF-7	breast:	n/a
8	chr6:31018523-31018573	PFSK-1	brain:	n/a
9	chr6:31018523-31018573	HCPEpiC	choroid plexus:	n/a
10	chr6:31018523-31018573	HEEpiC	esophagus:	n/a
11	chr6:31018523-31018573	AG04450	lung:	fetal
12	chr6:31018523-31018573	HUVEC	blood vessel:	n/a
13	chr6:31018523-31018573	T-47D	breast:	n/a
14	chr6:31018523-31018573	NT2-D1	testis:	n/a
15	chr6:31018523-31018573	HNPCEpiC	eye:	n/a
16	chr6:31018523-31018573	NHDF-neo	bronchial:	n/a
17	chr6:31018523-31018573	PANC-1	pancreas:	n/a
18	chr6:31018523-31018573	HRCEpiC	kidney:	n/a
19	chr6:31018523-31018573	AG04449	skin:	fetal
20	chr6:31018523-31018573	PrEC	prostate:	n/a
21	chr6:31018523-31018573	AoSMC	blood vessel:	n/a
22	chr6:31018523-31018573	GM12892	blood:	n/a
23	chr6:31018523-31018573	H1-hESC	embryonic stem cell:	embryo
24	chr6:31018523-31018573	IMR90	lung:	fetal
25	chr6:31018523-31018573	HRPEpiC	eye:	n/a
26	chr6:31018523-31018573	HL-60	blood:	n/a
27	chr6:31018523-31018573	GM19239	blood:	n/a
28	chr6:31018523-31018573	HPAEpiC	pulmonary alveolar:	n/a
29	chr6:31018523-31018573	GM06990	blood:	n/a
30	chr6:31018523-31018573	HRE	kidney:	n/a
31	chr6:31018523-31018573	SK-N-SH_RA	brain:	n/a
32	chr6:31018523-31018573	U87	brain:	n/a
33	chr6:31018523-31018573	NH-A	brain:	n/a
34	chr6:31018523-31018573	Hela-S3	cervix:	n/a
35	chr6:31018523-31018573	Jurkat	blood:	n/a
36	chr6:31018523-31018573	HCT-116	colon:	n/a
37	chr6:31018523-31018573	HIPEpiC	eye:	n/a
38	chr6:31018523-31018573	SK-N-MC	brain:	n/a
39	chr6:31018523-31018573	A549	lung:	n/a
40	chr6:31018523-31018573	AG10803	skin:	n/a
41	chr6:31018523-31018573	BE2_C	brain:	n/a
42	chr6:31018523-31018573	HMEC	breast:	n/a
43	chr6:31018523-31018573	HAEpiC	amniotic membrane:	n/a
44	chr6:31018523-31018573	CMK	blood:	n/a
45	chr6:31018523-31018573	Hepatocyte	liver:	n/a
46	chr6:31018523-31018573	GM12878	blood:	n/a
47	chr6:31018523-31018573	BJ	skin:	n/a
48	chr6:31018523-31018573	GM12891	blood:	n/a
49	chr6:31018523-31018573	AG09309	skin:	n/a
50	chr6:31018523-31018573	SAEC	small airway:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:31018538..31021131-chr6:31024335..31025981,2	K562	blood:
2	chr6:31010735..31013571-chr6:31016470..31018721,2	MCF-7	breast:
3	chr6:31013097..31015734-chr6:31016624..31018814,2	K562	blood:

No data

Variant related genes	Relation type
HCG22	CpG island

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs2251825	0.80[AFR][1000 genomes]
rs2251830	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2428517	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2508015	0.81[AMR][1000 genomes]
rs2517530	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517532	0.80[AFR][1000 genomes]
rs2517533	0.80[AFR][1000 genomes]
rs2523858	0.80[AFR][1000 genomes]
rs2523861	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2523862	0.80[AFR][1000 genomes]
rs2523865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523866	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523867	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs2844643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844644	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844645	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs3131926	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3519970	chr6:30382942-31378788	Genic enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
2	esv3519971	chr6:30382942-31378788	Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1030 gene(s)	inside rSNPs	diseases
3	nsv601481	chr6:30422632-31284253	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1012 gene(s)	inside rSNPs	diseases
4	nsv1015372	chr6:30704734-31582152	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
5	nsv538173	chr6:30704734-31582152	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
6	nsv1029442	chr6:31006647-31449207	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	82 gene(s)	inside rSNPs	diseases
7	nsv884130	chr6:31014305-31038756	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv884131	chr6:31014305-31040725	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv884132	chr6:31014305-31057183	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2523864	HCG22	cis	lymphoblastoid	seeQTL
rs2523864	HCG22	cis	Lymphoblastoid	GTEx
rs2523864	HIST1H3J	cis	parietal	SCAN
rs2523864	C6orf1	cis	parietal	SCAN
rs2523864	ZNF187	cis	cerebellum	SCAN
rs2523864	hmm31752	cis	multi-tissue	Pritchard
rs2523864	HCG27	cis	multi-tissue	Pritchard
rs2523864	HLA-DQB1	cis	multi-tissue	Pritchard

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:31009600-31027400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr6:31010600-31021600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:31013800-31021600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:31016200-31021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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