Variant report

Variant	rs7238729
Chromosome Location	chr18:29073191-29073192
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:50)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RELA	chr18:29073118-29073757	GM18951	blood:	n/a	n/a
2	CREB1	chr18:29073151-29073553	GM12878	blood:	n/a	n/a
3	BCL3	chr18:29073162-29073518	GM12878	blood:	n/a	n/a
4	NFATC1	chr18:29073104-29073519	GM12878	blood:	n/a	n/a
5	IRF4	chr18:29073186-29073700	GM12878	blood:	n/a	n/a
6	RUNX3	chr18:29073145-29073591	GM12878	blood:	n/a	n/a
7	EP300	chr18:29073118-29073449	GM12878	blood:	n/a	n/a
8	MTA3	chr18:29073145-29073570	GM12878	blood:	n/a	n/a
9	FOXM1	chr18:29073004-29073674	GM12878	blood:	n/a	n/a
10	BCL11A	chr18:29073153-29073684	GM12878	blood:	n/a	n/a
11	SPI1	chr18:29073136-29073585	GM12891	blood:	n/a	n/a
12	RELA	chr18:29073130-29073589	GM19193	blood:	n/a	n/a
13	PAX5	chr18:29073180-29073424	GM12878	blood:	n/a	n/a
14	SP1	chr18:29073102-29073559	GM12878	blood:	n/a	n/a
15	RELA	chr18:29073119-29073589	GM10847	blood:	n/a	n/a
16	MEF2A	chr18:29073092-29073524	GM12878	blood:	n/a	n/a
17	RELA	chr18:29073119-29073503	GM19099	blood:	n/a	n/a
18	TCF3	chr18:29073187-29073533	GM12878	blood:	n/a	n/a
19	STAT3	chr18:29073174-29073592	GM12878	blood:	n/a	n/a
20	RELA	chr18:29073120-29073589	GM15510	blood:	n/a	n/a
21	RELA	chr18:29073120-29073750	GM12878	blood:	n/a	n/a
22	EBF1	chr18:29073180-29073478	GM12878	blood:	n/a	n/a
23	TBL1XR1	chr18:29073163-29073467	GM12878	blood:	n/a	n/a
24	RELA	chr18:29073137-29073749	GM18505	blood:	n/a	n/a
25	NFIC	chr18:29073084-29073649	GM12878	blood:	n/a	n/a
26	IRF4	chr18:29073084-29073557	GM12878	blood:	n/a	n/a
27	EP300	chr18:29073074-29073588	GM12878	blood:	n/a	n/a
28	SP1	chr18:29073156-29073586	GM12878	blood:	n/a	n/a
29	NFIC	chr18:29073009-29073623	GM12878	blood:	n/a	n/a
30	EP300	chr18:29073178-29073483	GM12878	blood:	n/a	n/a
31	BCLAF1	chr18:29073175-29073475	GM12878	blood:	n/a	n/a
32	SPI1	chr18:29073103-29073691	GM12878	blood:	n/a	n/a
33	RUNX3	chr18:29073066-29073556	GM12878	blood:	n/a	n/a
34	CHD2	chr18:29073129-29073611	GM12878	blood:	n/a	n/a
35	NFATC1	chr18:29073071-29073511	GM12878	blood:	n/a	n/a
36	CREB1	chr18:29073106-29073610	GM12878	blood:	n/a	n/a
37	SPI1	chr18:29073160-29073519	GM12891	blood:	n/a	n/a
38	BCL11A	chr18:29073158-29073654	GM12878	blood:	n/a	n/a
39	PAX5	chr18:29073172-29073439	GM12878	blood:	n/a	n/a
40	POU2F2	chr18:29073181-29073454	GM12878	blood:	n/a	n/a
41	RELA	chr18:29073131-29073589	GM12891	blood:	n/a	n/a
42	BHLHE40	chr18:29073174-29073422	GM12878	blood:	n/a	n/a
43	ATF2	chr18:29073140-29073511	GM12878	blood:	n/a	n/a
44	PAX5	chr18:29073134-29073723	GM12878	blood:	n/a	n/a
45	PAX5	chr18:29073189-29073417	GM12878	blood:	n/a	n/a
46	POU2F2	chr18:29073128-29073690	GM12878	blood:	n/a	n/a
47	ATF2	chr18:29073036-29073485	GM12878	blood:	n/a	n/a
48	FOXM1	chr18:29073072-29073554	GM12878	blood:	n/a	n/a
49	EP300	chr18:29073083-29073899	GM12878	blood:	n/a	n/a
50	SPI1	chr18:29073101-29073550	GM12878	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr18:29065798..29067835-chr18:29072600..29075052,2	K562	blood:
2	chr18:29063380..29066106-chr18:29071423..29073407,2	K562	blood:
3	chr18:29070302..29073813-chr18:29076378..29079026,4	MCF-7	breast:
4	chr18:29070292..29073847-chr18:29075738..29079463,4	K562	blood:
5	chr18:29066393..29069517-chr18:29071339..29073369,4	K562	blood:

No data

Variant related genes	Relation type
DSG2	TF binding region
ENSG00000266521	Chromatin interaction
ENSG00000046604	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1031729	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1350731	0.96[ASN][1000 genomes]
rs1460602	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17660585	0.98[ASN][1000 genomes]
rs1824477	0.93[ASN][1000 genomes]
rs1841396	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2212617	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2212618	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2219584	0.96[ASN][1000 genomes]
rs2704050	0.92[ASN][1000 genomes]
rs2704051	0.94[ASN][1000 genomes]
rs2704052	0.95[ASN][1000 genomes]
rs2704053	0.95[ASN][1000 genomes]
rs2704055	0.86[ASN][1000 genomes]
rs2848677	0.95[ASN][1000 genomes]
rs2848680	0.95[ASN][1000 genomes]
rs2848681	0.95[ASN][1000 genomes]
rs4799310	0.98[ASN][1000 genomes]
rs4799573	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6506927	0.96[ASN][1000 genomes]
rs6506928	0.96[ASN][1000 genomes]
rs7227343	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7227984	0.98[ASN][1000 genomes]
rs7231288	0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7231553	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7232282	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7235272	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7236324	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7236469	0.98[ASN][1000 genomes]
rs7239805	0.87[ASN][1000 genomes]
rs7240824	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7240920	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7241107	0.93[ASN][1000 genomes]
rs73414280	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73953901	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9304097	0.96[ASN][1000 genomes]
rs9304098	0.87[ASN][1000 genomes]
rs9304099	0.98[ASN][1000 genomes]
rs9941421	0.93[ASN][1000 genomes]
rs9945031	0.98[ASN][1000 genomes]
rs9945420	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9951843	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9961910	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9961920	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9961925	0.98[ASN][1000 genomes]
rs9962121	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9962318	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9962333	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9962423	0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1066692	chr18:28856066-29190505	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543674	chr18:28856066-29190505	Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv916545	chr18:28898800-29166364	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv833615	chr18:29008396-29192976	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7238729	RP11-650P15.1	cis	Heart Left Ventricle	GTEx
rs7238729	RP11-650P15.1	cis	Thyroid	GTEx
rs7238729	DSG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29067600-29076800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr18:29069600-29073200	Weak transcription	Esophagus	oesophagus
3	chr18:29070600-29074400	Enhancers	GM12878-XiMat	blood
4	chr18:29071200-29077200	Weak transcription	Fetal Intestine Small	intestine
5	chr18:29071600-29073400	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr18:29071800-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:29071800-29077400	Weak transcription	HMEC	breast
8	chr18:29072000-29077200	Weak transcription	NHEK	skin
9	chr18:29072000-29077400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr18:29072200-29077600	Weak transcription	Placenta Amnion	Placenta Amnion

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links