Variant report

Variant	rs7181540
Chromosome Location	chr15:52042281-52042282
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:52041917-52044815	Raji	blood:	n/a	n/a
2	POLR2A	chr15:52042188-52043672	GM12891	blood:	n/a	n/a
3	RELA	chr15:52042201-52043746	GM12891	blood:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:52028180..52031136-chr15:52040562..52045385,6	MCF-7	breast:
2	chr15:52041956..52043686-chr15:52074164..52076601,2	MCF-7	breast:
3	chr15:52016515..52018648-chr15:52040542..52043046,2	MCF-7	breast:
4	chr15:52027363..52032665-chr15:52041435..52046045,23	MCF-7	breast:
5	chr15:52033609..52037215-chr15:52040115..52042966,3	MCF-7	breast:
6	chr15:52028355..52032748-chr15:52040539..52046492,10	K562	blood:
7	chr15:52040526..52042479-chr15:52043907..52045624,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000259377	TF binding region
TMOD2	TF binding region
ENSG00000259377	Chromatin interaction
ENSG00000140280	Chromatin interaction
ENSG00000128872	Chromatin interaction

Extended variants
information (count: 185 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:183)

rs_ID	r²[population]
rs1001690	0.93[CEU][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs1035737	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs10444824	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10444825	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10851503	0.83[EUR][1000 genomes]
rs10851504	0.80[EUR][1000 genomes]
rs11049	1.00[CEU][hapmap];0.82[CHB][hapmap]
rs11070865	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11070866	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070867	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070868	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11070869	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1133883	1.00[CEU][hapmap]
rs11630253	0.80[EUR][1000 genomes]
rs11630579	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11630943	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11631858	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636869	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11637876	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12050524	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12591672	0.80[EUR][1000 genomes]
rs12593708	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs12901638	0.81[EUR][1000 genomes]
rs12903500	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12904413	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12904900	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12905283	1.00[CEU][hapmap];0.81[CHB][hapmap];0.88[EUR][1000 genomes]
rs12908327	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12912928	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12913583	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12913850	0.83[EUR][1000 genomes]
rs12915015	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs12915568	1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[EUR][1000 genomes]
rs17526463	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17526760	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17539905	0.80[EUR][1000 genomes]
rs17610862	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17611193	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1840708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1863430	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1991267	0.85[CEU][hapmap]
rs2006773	0.83[EUR][1000 genomes]
rs2007335	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2007355	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2009972	0.89[CEU][hapmap]
rs2010026	1.00[CEU][hapmap];0.81[CHB][hapmap];0.91[EUR][1000 genomes]
rs2011995	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2034856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2052705	1.00[CEU][hapmap]
rs2052706	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2052708	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2052709	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2114191	1.00[CEU][hapmap]
rs2252606	1.00[CEU][hapmap]
rs2252831	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2253116	1.00[CEU][hapmap]
rs2303443	0.95[CHB][hapmap]
rs2414122	0.84[CEU][hapmap]
rs2433217	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2433221	0.96[CEU][hapmap]
rs2433222	0.80[EUR][1000 genomes]
rs2436655	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2436656	1.00[CEU][hapmap]
rs2436657	0.80[EUR][1000 genomes]
rs2436660	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2436662	0.83[EUR][1000 genomes]
rs2441780	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2448946	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2448947	0.81[EUR][1000 genomes]
rs2448948	0.81[EUR][1000 genomes]
rs2448950	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2448951	0.81[EUR][1000 genomes]
rs2448953	1.00[CEU][hapmap]
rs2470600	0.81[EUR][1000 genomes]
rs2470601	0.81[EUR][1000 genomes]
rs2470608	0.81[EUR][1000 genomes]
rs2470610	0.81[EUR][1000 genomes]
rs2470611	0.80[EUR][1000 genomes]
rs2470612	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs2470618	0.80[EUR][1000 genomes]
rs2554314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2554327	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2554328	0.83[EUR][1000 genomes]
rs2554348	0.89[CEU][hapmap]
rs2554349	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2554350	0.80[EUR][1000 genomes]
rs2554353	0.83[EUR][1000 genomes]
rs2570238	0.83[EUR][1000 genomes]
rs2570239	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2570241	1.00[CEU][hapmap]
rs2570248	0.83[EUR][1000 genomes]
rs2593168	0.80[EUR][1000 genomes]
rs2593170	1.00[CEU][hapmap]
rs2593173	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2593181	0.83[CEU][hapmap]
rs2593182	0.80[EUR][1000 genomes]
rs2593183	0.80[EUR][1000 genomes]
rs2593199	1.00[CEU][hapmap]
rs2593202	1.00[CEU][hapmap]
rs2623266	0.80[EUR][1000 genomes]
rs2623271	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs2623279	0.80[EUR][1000 genomes]
rs2623281	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2623282	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2623283	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2623284	0.80[EUR][1000 genomes]
rs2623285	0.80[EUR][1000 genomes]
rs2623286	0.80[EUR][1000 genomes]
rs28699115	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2912186	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2912187	1.00[CEU][hapmap]
rs2912189	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2916169	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2916172	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2916175	0.81[EUR][1000 genomes]
rs2916176	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2916177	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2921951	0.80[EUR][1000 genomes]
rs2921953	0.81[EUR][1000 genomes]
rs2929423	1.00[CEU][hapmap];0.80[EUR][1000 genomes]
rs2929424	1.00[CEU][hapmap]
rs2929425	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2929426	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2929428	0.80[EUR][1000 genomes]
rs2959285	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2959298	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2959299	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs2959300	0.81[EUR][1000 genomes]
rs2959305	0.81[EUR][1000 genomes]
rs2959307	0.81[EUR][1000 genomes]
rs3088312	0.92[EUR][1000 genomes]
rs34098740	0.86[ASN][1000 genomes]
rs34504520	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35270232	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35391204	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35823585	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36087956	0.81[EUR][1000 genomes]
rs3794532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3898905	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4365237	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55887408	0.86[AMR][1000 genomes]
rs56148956	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56185947	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62016192	0.80[EUR][1000 genomes]
rs6493520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6493521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493525	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6493526	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs7162176	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7162925	1.00[CEU][hapmap];0.83[CHB][hapmap]
rs7163541	1.00[CEU][hapmap];0.81[CHB][hapmap]
rs7164961	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166962	0.93[EUR][1000 genomes]
rs7168659	1.00[CEU][hapmap];0.82[YRI][hapmap];0.93[EUR][1000 genomes]
rs7170091	1.00[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170910	0.82[EUR][1000 genomes]
rs7171516	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7171796	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7174497	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7174808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7175017	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7178166	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178561	1.00[CEU][hapmap];0.86[CHB][hapmap];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7178776	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7178940	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7179599	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs726158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72732914	0.81[EUR][1000 genomes]
rs8024585	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8025069	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026521	0.89[EUR][1000 genomes]
rs8027721	0.82[EUR][1000 genomes]
rs8028486	0.85[EUR][1000 genomes]
rs8028922	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033433	0.83[EUR][1000 genomes]
rs8035126	0.82[EUR][1000 genomes]
rs8035173	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs8038344	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs8040975	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040986	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8040991	0.83[EUR][1000 genomes]
rs990665	0.80[EUR][1000 genomes]
rs9944235	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[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	esv2830011	chr15:52027777-52048710	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a
2	nsv569409	chr15:52028914-52268144	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7181540	SCG3	cis	Frontal Cortex	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52030600-52043200	Weak transcription	Gastric	stomach
2	chr15:52031200-52043000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:52041400-52042600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:52041600-52042800	Enhancers	K562	blood
5	chr15:52042200-52042600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
6	chr15:52042200-52042600	Enhancers	GM12878-XiMat	blood
7	chr15:52042200-52043000	Enhancers	Primary B cells from peripheral blood	blood

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