Variant report

Variant	rs4375365
Chromosome Location	chr10:49866453-49866454
allele	A/G
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	CTCF	chr10:49866352-49866631	LNCaP	prostate:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
2	CTCF	chr10:49866328-49866638	Medullo	brain:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
3	REST	chr10:49866331-49866700	K562	blood:	n/a	chr10:49866578-49866587
4	MAZ	chr10:49866437-49866636	HepG2	liver:	n/a	n/a
5	RCOR1	chr10:49866319-49866676	K562	blood:	n/a	n/a
6	CTCF	chr10:49866420-49866570	AG09319	gingival:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
7	CTCF	chr10:49866354-49866606	SK-N-SH_RA	brain:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
8	REST	chr10:49866316-49866649	PFSK-1	brain:	n/a	chr10:49866578-49866587
9	STAT1	chr10:49866416-49866623	GM12878	blood:	n/a	n/a
10	CTCF	chr10:49866400-49866550	GM12871	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
11	CTCF	chr10:49866400-49866550	Caco-2	colon:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
12	CTCF	chr10:49865780-49867068	SK-N-SH	brain:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49865880-49865887 chr10:49866485-49866503
13	CTCF	chr10:49866420-49866570	AG04449	skin:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
14	CTCF	chr10:49866420-49866570	HPAF	blood vessel:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
15	BCLAF1	chr10:49866315-49866715	GM12878	blood:	n/a	n/a
16	CTCF	chr10:49866400-49866550	AoAF	blood vessel:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
17	RAD21	chr10:49866229-49866666	HepG2	liver:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
18	CTCF	chr10:49866391-49866646	MCF-7	breast:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
19	CTCF	chr10:49866348-49866626	GM10266	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
20	CTCF	chr10:49866400-49866550	GM12869	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
21	CTCF	chr10:49866440-49866590	NHLF	lung:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
22	WRNIP1	chr10:49866345-49866625	GM12878	blood:	n/a	n/a
23	CTCF	chr10:49866420-49866570	HCPEpiC	choroid plexus:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
24	RAD21	chr10:49866049-49866714	IMR90	lung:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
25	GABPA	chr10:49866421-49866744	K562	blood:	n/a	n/a
26	CTCF	chr10:49866420-49866570	HAc	cerebellar:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
27	CTCF	chr10:49866400-49866550	MCF-7	breast:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
28	CTCF	chr10:49866440-49866590	GM12874	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
29	CTCF	chr10:49866358-49866614	HepG2	liver:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
30	CTCF	chr10:49866380-49866530	GM12871	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
31	RAD21	chr10:49866373-49866612	K562	blood:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
32	CTCF	chr10:49866420-49866570	GM06990	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
33	ZNF143	chr10:49866321-49866712	H1-hESC	embryonic stem cell:	n/a	n/a
34	CHD2	chr10:49866430-49866620	HepG2	liver:	n/a	n/a
35	SMC3	chr10:49866311-49866758	K562	blood:	n/a	chr10:49866487-49866501
36	RAD21	chr10:49866164-49866876	HCT-116	colon:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
37	CTCF	chr10:49866420-49866570	HUVEC	blood vessel:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
38	REST	chr10:49866323-49866717	H1-hESC	embryonic stem cell:	n/a	chr10:49866578-49866587
39	RAD21	chr10:49866178-49866840	MCF-7	breast:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
40	SMC3	chr10:49866309-49866730	Hela-S3	cervix:	n/a	chr10:49866487-49866501
41	REST	chr10:49866366-49866707	H1-hESC	embryonic stem cell:	n/a	chr10:49866578-49866587
42	RAD21	chr10:49866214-49866702	Hela-S3	cervix:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
43	CTCF	chr10:49866175-49866868	MCF-7	breast:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
44	RAD21	chr10:49866266-49866838	H1-hESC	embryonic stem cell:	n/a	chr10:49866486-49866505 chr10:49866487-49866501
45	CTCF	chr10:49866440-49866590	SK-N-SH_RA	brain:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
46	YY1	chr10:49866347-49866627	H1-hESC	embryonic stem cell:	n/a	n/a
47	CTCF	chr10:49865445-49867158	A549	lung:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49865880-49865887 chr10:49866485-49866503
48	CTCF	chr10:49866400-49866550	GM12864	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
49	CTCF	chr10:49866355-49866610	A549	lung:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503
50	CTCF	chr10:49866380-49866530	GM12866	blood:	n/a	chr10:49866486-49866502 chr10:49866487-49866508 chr10:49866488-49866501 chr10:49866485-49866503

No.	Distal block	Cell Line	Cell type
1	chr10:49866052..49867979-chr10:50372361..50373055,5	MCF-7	breast:
2	chr10:49863839..49866724-chr10:50507173..50508742,2	K562	blood:
3	chr10:49865954..49866714-chr10:50369332..50370327,2	MCF-7	breast:
4	chr10:49866375..49866922-chr10:50726828..50727744,2	K562	blood:
5	chr10:49866085..49866961-chr10:50720002..50720537,2	K562	blood:
6	chr10:49866337..49866979-chr10:49950144..49951064,2	K562	blood:
7	chr10:49730097..49732596-chr10:49864867..49867280,2	K562	blood:
8	chr10:49866246..49867060-chr10:50086583..50087265,3	MCF-7	breast:

Variant related genes	Relation type
ARHGAP22	TF binding region
ENSG00000128805	Chromatin interaction
ENSG00000177354	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10857616	0.82[ASN][1000 genomes]
rs11101416	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12257645	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377595	0.85[CHD][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs2377596	0.85[ASN][1000 genomes]
rs2377612	0.91[ASN][1000 genomes]
rs2377613	0.91[ASN][1000 genomes]
rs2377614	0.91[ASN][1000 genomes]
rs2377615	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377616	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2377618	0.90[EUR][1000 genomes]
rs4240515	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4373841	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4525142	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4562728	0.80[ASW][hapmap];0.88[CHD][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap];0.88[ASN][1000 genomes]
rs7087882	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7087885	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7911516	0.90[EUR][1000 genomes];0.81[ASN][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	nsv895371	chr10:49492075-50232180	Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
2	nsv895372	chr10:49576878-49933488	Enhancers Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4375365	FRMPD2	cis	parietal	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:49865200-49866800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr10:49865200-49879200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr10:49866000-49866800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr10:49866000-49866800	Enhancers	Brain Substantia Nigra	brain
5	chr10:49866000-49867000	Enhancers	Primary B cells from peripheral blood	blood
6	chr10:49866200-49866600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr10:49866400-49866600	Enhancers	Primary B cells from cord blood	blood
8	chr10:49866400-49866600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr10:49866400-49866600	Enhancers	Brain Anterior Caudate	brain
10	chr10:49866400-49866600	Bivalent/Poised TSS	Fetal Kidney	kidney
11	chr10:49866400-49867000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links