Variant report

Variant	rs4695069
Chromosome Location	chr4:45007208-45007209
allele	G/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	STAT3	chr4:45006953-45007272	MCF10A-Er-Src	breast:	n/a	n/a
2	RUNX3	chr4:45007183-45007597	GM12878	blood:	n/a	n/a
3	EP300	chr4:45007061-45007463	GM12878	blood:	n/a	n/a
4	FOS	chr4:45006934-45007248	MCF10A-Er-Src	breast:	n/a	chr4:45007110-45007118 chr4:45007108-45007120
5	STAT3	chr4:45006931-45007239	MCF10A-Er-Src	breast:	n/a	n/a
6	NFIC	chr4:45006971-45007473	GM12878	blood:	n/a	n/a
7	POLR2A	chr4:45006975-45007368	H1-neurons	neurons:	n/a	n/a
8	FOS	chr4:45006927-45007497	MCF10A-Er-Src	breast:	n/a	chr4:45007110-45007118 chr4:45007447-45007459 chr4:45007108-45007120
9	POLR2A	chr4:45007001-45007384	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:44999456..45001286-chr4:45006123..45008246,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248744	TF binding region

Extended variants
information (count: 109 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10000940	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10001739	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10003579	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10003776	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10003984	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10004173	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10006643	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10009882	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10031439	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10034588	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433683	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10433684	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10938378	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11723797	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11726237	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11727488	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11730391	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11734842	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12501461	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12502784	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12504288	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12505440	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12509759	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12512128	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12512173	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12512921	0.91[ASN][1000 genomes]
rs13114174	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13123198	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13123623	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13125752	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13143643	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13145245	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28683174	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28712193	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34298665	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34725881	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34771773	0.81[ASN][1000 genomes]
rs35739449	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4267770	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4280774	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4312794	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4377625	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4410559	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4431264	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447894	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4456993	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4464602	0.82[AFR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4467605	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4481265	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4492035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505863	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4558900	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4560452	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4571371	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4580687	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4621472	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4629490	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4632690	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4635847	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4639112	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4695070	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62409744	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411580	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62411584	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447395	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447396	0.92[ASN][1000 genomes]
rs6447397	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447398	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6447399	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447400	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6447401	0.85[ASN][1000 genomes]
rs6447402	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6820860	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6822744	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6823641	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6832190	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6839710	0.87[ASN][1000 genomes]
rs6848088	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848089	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6848542	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6855537	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7677319	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7678059	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7679461	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682854	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7698277	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7699473	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531944	chr4:44299343-45200700	Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv1014327	chr4:44735209-45218149	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv878979	chr4:44871931-45102488	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv432591	chr4:44922068-45017576	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv432594	chr4:44932945-45033572	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv432595	chr4:44951672-45010972	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
7	nsv432596	chr4:44951672-45037672	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv2757056	chr4:44960444-45033572	Enhancers Weak transcription ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv2759250	chr4:44960444-45033572	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv878980	chr4:44961533-45015525	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv878981	chr4:44961533-45018583	Enhancers ZNF genes & repeats Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv2763861	chr4:44964479-45011262	Weak transcription Enhancers ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
13	nsv10488	chr4:44965278-45011616	Enhancers Strong transcription Weak transcription ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
14	nsv1013463	chr4:44967004-45013835	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1005572	chr4:44967004-45017576	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
16	nsv432597	chr4:44968572-45010972	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
17	esv2752047	chr4:44968572-45072206	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
18	nsv594102	chr4:44968603-45007208	Weak transcription Enhancers Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a
19	nsv878982	chr4:44982938-45031256	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
20	nsv878983	chr4:44982938-45039597	Enhancers Weak transcription Flanking Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
21	esv1830314	chr4:44983899-45023201	Enhancers Weak transcription Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
22	esv1807059	chr4:45005852-45010969	Enhancers Weak transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4695069	GNPDA2	cis	cerebellum	SCAN
rs4695069	TMEM33	cis	parietal	SCAN
rs4695069	GABRG1	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:45006200-45008400	Enhancers	HMEC	breast
2	chr4:45006200-45008600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr4:45006400-45007400	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr4:45006600-45007400	Enhancers	iPS-20b Cell Line	embryonic stem cell
5	chr4:45006800-45007400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr4:45007200-45007400	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr4:45007200-45007400	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr4:45007200-45007400	Enhancers	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links