Variant report

Variant	rs56998970
Chromosome Location	chr7:150004488-150004489
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:35)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:35 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUND	chr7:150004390-150004577	HepG2	liver:	n/a	n/a
2	TEAD4	chr7:150004174-150004670	K562	blood:	n/a	n/a
3	MAX	chr7:150004267-150004575	K562	blood:	n/a	n/a
4	MAX	chr7:150004363-150004492	K562	blood:	n/a	n/a
5	USF2	chr7:150004421-150004546	Hela-S3	cervix:	n/a	n/a
6	YY1	chr7:150004310-150004546	K562	blood:	n/a	n/a
7	GATA2	chr7:150004223-150004652	K562	blood:	n/a	n/a
8	RUNX3	chr7:150004274-150004534	GM12878	blood:	n/a	n/a
9	BRCA1	chr7:150004406-150004492	Hela-S3	cervix:	n/a	n/a
10	NR2F2	chr7:150004173-150004649	K562	blood:	n/a	n/a
11	USF1	chr7:150004447-150004652	HepG2	liver:	n/a	n/a
12	EP300	chr7:150004249-150004549	K562	blood:	n/a	n/a
13	KAP1	chr7:150004021-150004810	K562	blood:	n/a	n/a
14	MYC	chr7:150004343-150004531	K562	blood:	n/a	n/a
15	CBX3	chr7:150004239-150004629	K562	blood:	n/a	n/a
16	CBX3	chr7:150004208-150004572	HCT-116	colon:	n/a	n/a
17	BHLHE40	chr7:150004337-150004505	K562	blood:	n/a	n/a
18	NR2F2	chr7:150004087-150004711	K562	blood:	n/a	n/a
19	RCOR1	chr7:150004339-150004553	K562	blood:	n/a	n/a
20	ZNF143	chr7:150004339-150004542	K562	blood:	n/a	n/a
21	JUND	chr7:150004340-150004540	K562	blood:	n/a	n/a
22	POLR2A	chr7:150004366-150004657	Hela-S3	cervix:	n/a	n/a
23	TRIM28	chr7:150004278-150004587	K562	blood:	n/a	n/a
24	USF1	chr7:150004440-150004659	HepG2	liver:	n/a	n/a
25	SP1	chr7:150004354-150004743	HepG2	liver:	n/a	n/a
26	CEBPB	chr7:150004309-150004607	Hela-S3	cervix:	n/a	n/a
27	CBX3	chr7:150004138-150004672	K562	blood:	n/a	n/a
28	FOSL2	chr7:150004377-150004735	HepG2	liver:	n/a	n/a
29	SETDB1	chr7:150003971-150004529	U2OS	brain:	n/a	n/a
30	ATF1	chr7:150004234-150004547	K562	blood:	n/a	n/a
31	RXRA	chr7:150004377-150004672	HepG2	liver:	n/a	n/a
32	ZNF143	chr7:150004425-150004500	Hela-S3	cervix:	n/a	n/a
33	TRIM28	chr7:150004123-150004662	K562	blood:	n/a	n/a
34	FOXA1	chr7:150004335-150004755	HepG2	liver:	n/a	n/a
35	TAL1	chr7:150004307-150004507	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr7:150002516..150004738-chr7:150017976..150020518,2	K562	blood:
2	chr7:150003788..150006557-chr7:150126189..150128283,2	K562	blood:
3	chr7:150002193..150004738-chr7:150017976..150020637,3	K562	blood:
4	chr7:150004469..150007293-chr7:150009416..150012608,5	K562	blood:

No data

Variant related genes	Relation type
ACTR3C	TF binding region
ENSG00000106526	Chromatin interaction
ENSG00000127399	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10952249	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10952250	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11764936	0.85[EUR][1000 genomes]
rs11765644	0.86[EUR][1000 genomes]
rs11765692	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11766288	0.90[EUR][1000 genomes]
rs11767726	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11769348	0.85[EUR][1000 genomes]
rs11773351	0.84[EUR][1000 genomes]
rs11974980	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11975886	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11983355	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1464752	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1464753	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17837498	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1916932	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1962004	0.88[EUR][1000 genomes]
rs1983440	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2108851	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108852	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108853	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2108854	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159234	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2159235	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2159236	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2373751	0.86[EUR][1000 genomes]
rs3088207	0.83[EUR][1000 genomes]
rs3735169	0.83[EUR][1000 genomes]
rs3735170	0.83[EUR][1000 genomes]
rs3735171	0.84[EUR][1000 genomes]
rs3735172	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3735173	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3735174	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3735175	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3800780	0.86[EUR][1000 genomes]
rs3800781	0.86[EUR][1000 genomes]
rs4395803	0.85[EUR][1000 genomes]
rs4554381	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55715989	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55881542	0.85[EUR][1000 genomes]
rs56019796	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56190213	0.85[EUR][1000 genomes]
rs56402329	0.81[EUR][1000 genomes]
rs56923535	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57888387	0.93[EUR][1000 genomes]
rs59572505	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60268791	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60283368	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60467296	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73170169	0.93[EUR][1000 genomes]
rs73170174	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs73170185	0.86[EUR][1000 genomes]
rs7781827	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7788316	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7806429	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[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	nsv889435	chr7:149585379-150013393	ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1034409	chr7:149844639-150447071	Flanking Active TSS Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	75 gene(s)	inside rSNPs	diseases
3	nsv608990	chr7:149961274-150707488	Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
4	nsv1015582	chr7:149967986-150285104	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
5	nsv981608	chr7:150002640-150009746	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs56998970	ZBED6CL	cis	Esophagus Mucosa	GTEx
rs56998970	LRRC61	Cis_1M	lymphoblastoid	RTeQTL
rs56998970	C7orf29	Cis_1M	lymphoblastoid	RTeQTL
rs56998970	ZBED6CL	cis	Esophagus Muscularis	GTEx
rs56998970	LRRC61	cis	Thyroid	GTEx
rs56998970	LRRC61	cis	Skin Sun Exposed Lower leg	GTEx
rs56998970	LRRC61	cis	Muscle Skeletal	GTEx
rs56998970	ACTR3C	cis	Muscle Skeletal	GTEx
rs56998970	LRRC61	cis	Esophagus Mucosa	GTEx
rs56998970	LRRC61	cis	Nerve Tibial	GTEx
rs56998970	LRRC61	cis	Whole Blood	GTEx
rs56998970	RARRES2	cis	multi-tissue	Pritchard

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:149984200-150012400	Weak transcription	Liver	Liver
2	chr7:149984200-150019400	Weak transcription	Colonic Mucosa	Colon
3	chr7:149992400-150018000	Weak transcription	Fetal Intestine Small	intestine
4	chr7:150000400-150006600	Enhancers	K562	blood
5	chr7:150001800-150005000	Enhancers	Hela-S3	cervix
6	chr7:150002600-150004600	Weak transcription	HepG2	liver
7	chr7:150002600-150007200	Weak transcription	Pancreas	Pancrea
8	chr7:150003800-150016000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr7:150004000-150019000	Weak transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links