Variant report

Variant	rs2517597
Chromosome Location	chr6:30081189-30081190
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	GATA3	chr6:30080728-30081344	MCF-7	breast:	n/a	chr6:30080737-30080747
2	RELA	chr6:30080489-30081505	GM19193	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
3	SP1	chr6:30080827-30081252	GM12878	blood:	n/a	n/a
4	RELA	chr6:30080835-30081422	GM19099	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
5	TCF12	chr6:30080679-30081230	A549	lung:	n/a	n/a
6	RUNX3	chr6:30080859-30081400	GM12878	blood:	n/a	n/a
7	EBF1	chr6:30080865-30081420	GM12878	blood:	n/a	n/a
8	IKZF1	chr6:30081116-30081388	GM12878	blood:	n/a	n/a
9	HNF4A	chr6:30080760-30081196	HepG2	liver:	n/a	chr6:30080912-30080927 chr6:30080913-30080927 chr6:30080914-30080926 chr6:30080913-30080927 chr6:30081089-30081102 chr6:30080918-30080926 chr6:30080912-30080927 chr6:30080914-30080926 chr6:30081089-30081102 chr6:30080913-30080925 chr6:30080914-30080926 chr6:30080911-30080929 chr6:30080913-30080926 chr6:30080912-30080927 chr6:30080914-30080927
10	WRNIP1	chr6:30081029-30081225	GM12878	blood:	n/a	n/a
11	SP1	chr6:30080692-30081239	A549	lung:	n/a	n/a
12	RELA	chr6:30080784-30081392	GM12878	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
13	CEBPB	chr6:30080767-30081257	MCF-7	breast:	n/a	chr6:30080993-30081004
14	RELA	chr6:30080853-30081333	GM12892	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
15	RELA	chr6:30080467-30081547	GM12891	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
16	RELA	chr6:30080848-30081528	GM18505	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
17	RELA	chr6:30080915-30081360	GM18951	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
18	CEBPB	chr6:30080857-30081204	A549	lung:	n/a	chr6:30080993-30081004
19	POU2F2	chr6:30080886-30081271	GM12891	blood:	n/a	chr6:30081085-30081103
20	RELA	chr6:30080879-30081332	GM15510	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
21	EP300	chr6:30080823-30081280	GM12878	blood:	n/a	n/a
22	EBF1	chr6:30080832-30081238	GM12878	blood:	n/a	n/a
23	RELA	chr6:30080827-30081389	GM10847	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000
24	EP300	chr6:30080739-30081277	MCF-7	breast:	n/a	chr6:30080761-30080775
25	EBF1	chr6:30080840-30081271	GM12878	blood:	n/a	n/a
26	NR2F2	chr6:30080772-30081425	MCF-7	breast:	n/a	chr6:30081045-30081060
27	RELA	chr6:30080820-30081335	GM18526	blood:	n/a	chr6:30081212-30081221 chr6:30080991-30081000 chr6:30081212-30081221 chr6:30080991-30081000

No.	Distal block	Cell Line	Cell type
1	chr6:30072138..30074365-chr6:30079433..30082098,2	K562	blood:
2	chr6:30080946..30082589-chr6:30093243..30095341,2	MCF-7	breast:
3	chr6:30072893..30076173-chr6:30078690..30081417,3	MCF-7	breast:

Variant related genes	Relation type
TRIM31	TF binding region
ENSG00000204616	Chromatin interaction
ENSG00000231226	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1034326	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1034327	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1541269	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2239529	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2245420	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2249099	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2427749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517595	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517596	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2517598	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523976	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523977	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523979	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523981	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523982	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523983	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523984	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523985	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2523986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523988	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2523989	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2523992	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2844790	0.93[EUR][1000 genomes]
rs2844791	0.81[EUR][1000 genomes]
rs2844792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2844793	0.87[EUR][1000 genomes];0.92[ASN][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	nsv884055	chr6:30078275-30087776	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2517597	ZNF192	cis	parietal	SCAN
rs2517597	ZNF323	cis	parietal	SCAN
rs2517597	ZNF192	cis	cerebellum	SCAN
rs2517597	ZKSCAN3	cis	parietal	SCAN
rs2517597	ZNF193	cis	cerebellum	SCAN
rs2517597	HLA-C	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30078400-30081400	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr6:30080000-30081200	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
3	chr6:30080000-30081800	Enhancers	Liver	Liver
4	chr6:30080200-30082400	Enhancers	HepG2	liver
5	chr6:30080600-30081200	Weak transcription	Stomach Mucosa	stomach
6	chr6:30080600-30081800	Flanking Active TSS	GM12878-XiMat	blood
7	chr6:30080800-30081200	Active TSS	A549	lung
8	chr6:30080800-30081400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
9	chr6:30080800-30082800	Enhancers	Fetal Intestine Large	intestine
10	chr6:30080800-30082800	Enhancers	Fetal Intestine Small	intestine
11	chr6:30081000-30081200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
12	chr6:30081000-30081200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
13	chr6:30081000-30081200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr6:30081000-30081400	Flanking Active TSS	Colonic Mucosa	Colon
15	chr6:30081000-30081400	Flanking Active TSS	Duodenum Mucosa	Duodenum
16	chr6:30081000-30081400	Flanking Active TSS	Hela-S3	cervix

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