Variant report

Variant	rs13090194
Chromosome Location	chr3:46069573-46069574
allele	A/C
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	POLR2A	chr3:46069316-46069712	U87	brain:	n/a	n/a
2	JUND	chr3:46069384-46069581	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr3:46069316-46069657	U87	brain:	n/a	n/a
4	CBX3	chr3:46069507-46069824	K562	blood:	n/a	n/a
5	ZNF143	chr3:46069530-46069780	K562	blood:	n/a	n/a
6	CTCF	chr3:46069544-46069889	K562	blood:	n/a	n/a
7	KAP1	chr3:46069327-46070043	K562	blood:	n/a	n/a
8	SETDB1	chr3:46069436-46069960	U2OS	brain:	n/a	n/a
9	RCOR1	chr3:46069545-46069738	K562	blood:	n/a	n/a
10	CBX3	chr3:46069517-46069913	K562	blood:	n/a	n/a

Variant related genes	Relation type
XCR1	TF binding region

Extended variants
information (count: 192 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:187)

rs_ID	r²[population]
rs1078355	0.89[AFR][1000 genomes]
rs12108042	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13059238	0.83[EUR][1000 genomes]
rs13060287	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13063527	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13066062	0.87[EUR][1000 genomes]
rs13066516	0.83[EUR][1000 genomes]
rs13068410	0.88[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13068570	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13069079	1.00[CEU][hapmap];0.93[GIH][hapmap];0.86[EUR][1000 genomes]
rs13069742	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13071283	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13072267	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13074382	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13075528	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13075758	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13078739	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs13079869	1.00[CEU][hapmap];0.95[GIH][hapmap];0.81[TSI][hapmap];0.87[EUR][1000 genomes]
rs13081151	0.99[EUR][1000 genomes]
rs13081213	0.93[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082697	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13089554	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13089855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13091868	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13093179	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13094262	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs13095602	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13095717	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13096741	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13097556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13098366	0.82[ASN][1000 genomes]
rs13099120	0.83[EUR][1000 genomes]
rs13433997	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1491950	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1491951	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17214952	1.00[CEU][hapmap];0.95[GIH][hapmap];0.86[EUR][1000 genomes]
rs17215008	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs17215981	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17280623	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs17330872	1.00[CEU][hapmap];0.97[GIH][hapmap];0.81[TSI][hapmap];0.90[EUR][1000 genomes]
rs17714101	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs17714228	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs17764831	0.89[CEU][hapmap]
rs17764980	0.89[CEU][hapmap];0.80[EUR][1000 genomes]
rs1994491	0.89[CEU][hapmap];0.81[EUR][1000 genomes]
rs1994492	0.82[EUR][1000 genomes]
rs1994493	0.82[EUR][1000 genomes]
rs2088690	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088691	0.84[AFR][1000 genomes]
rs2088692	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2088693	0.90[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2102055	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2102056	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2171531	0.84[EUR][1000 genomes]
rs2230322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276856	0.90[YRI][hapmap]
rs2373087	0.83[EUR][1000 genomes]
rs33910087	0.87[EUR][1000 genomes]
rs34000569	0.86[EUR][1000 genomes]
rs34047915	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34068335	0.82[EUR][1000 genomes]
rs34093271	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34127208	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34168660	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34283240	0.96[EUR][1000 genomes]
rs34324101	0.86[EUR][1000 genomes]
rs34339943	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34340587	0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34381952	0.85[EUR][1000 genomes]
rs34438204	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34442130	0.89[EUR][1000 genomes]
rs34452002	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34460587	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34492478	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34493660	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34562820	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34584867	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34619093	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34679077	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34718164	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34754340	0.96[EUR][1000 genomes]
rs34766614	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34774687	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34805664	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34836513	0.96[EUR][1000 genomes]
rs34849862	0.86[EUR][1000 genomes]
rs34863575	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34867672	0.88[EUR][1000 genomes]
rs34924300	0.86[EUR][1000 genomes]
rs35028116	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs35110864	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35159820	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35161099	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35209528	0.86[EUR][1000 genomes]
rs35334665	0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35454877	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35464221	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35477280	0.83[EUR][1000 genomes]
rs35501575	0.86[EUR][1000 genomes]
rs35516580	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35525815	0.86[EUR][1000 genomes]
rs35539222	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35669129	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35751180	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35772789	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35814488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35827997	0.85[EUR][1000 genomes]
rs35831747	0.83[EUR][1000 genomes]
rs35855315	0.86[EUR][1000 genomes]
rs35883205	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35921206	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35930050	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35951367	0.82[ASN][1000 genomes]
rs36023124	0.96[EUR][1000 genomes]
rs36039366	0.85[EUR][1000 genomes]
rs36040135	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36057789	0.93[EUR][1000 genomes]
rs36122610	0.89[EUR][1000 genomes]
rs3851346	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41289616	0.85[EUR][1000 genomes]
rs41289622	0.87[EUR][1000 genomes]
rs4339140	0.91[ASN][1000 genomes]
rs4362758	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4373103	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4388012	1.00[CEU][hapmap];0.90[GIH][hapmap];0.85[EUR][1000 genomes]
rs4683166	0.88[EUR][1000 genomes]
rs55743140	0.89[AFR][1000 genomes]
rs55875328	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55920693	0.83[EUR][1000 genomes]
rs56071453	0.83[AFR][1000 genomes]
rs56332428	0.85[EUR][1000 genomes]
rs56738797	0.85[AFR][1000 genomes]
rs57636813	0.88[AFR][1000 genomes]
rs58139750	0.89[AFR][1000 genomes]
rs58969771	0.89[AFR][1000 genomes]
rs59676542	0.81[AFR][1000 genomes]
rs60019065	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60080146	0.89[AFR][1000 genomes]
rs61201782	0.90[AFR][1000 genomes]
rs61276379	0.88[AFR][1000 genomes]
rs61556067	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61598729	0.89[AFR][1000 genomes]
rs61650989	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67200151	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6780028	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6785091	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs6790866	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791016	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67937868	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68087193	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71325092	0.80[EUR][1000 genomes]
rs71325095	0.85[EUR][1000 genomes]
rs71325096	0.86[EUR][1000 genomes]
rs71325098	0.87[EUR][1000 genomes]
rs71325100	0.87[EUR][1000 genomes]
rs71325101	0.85[EUR][1000 genomes]
rs71325102	0.86[EUR][1000 genomes]
rs71327003	0.96[EUR][1000 genomes]
rs71327006	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327007	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327009	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71327010	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71327014	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71327015	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71327017	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71327021	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71327023	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71327024	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71327025	0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs71615438	0.96[EUR][1000 genomes]
rs72885402	0.89[AFR][1000 genomes]
rs72887108	0.89[AFR][1000 genomes]
rs72887131	0.90[AFR][1000 genomes]
rs72899100	0.88[AFR][1000 genomes]
rs73830713	0.85[AFR][1000 genomes]
rs73833519	0.87[AFR][1000 genomes]
rs751667	0.86[YRI][hapmap]
rs7642229	0.86[EUR][1000 genomes]
rs7642320	0.88[EUR][1000 genomes]
rs7652478	0.88[EUR][1000 genomes]
rs876668	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9824651	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9825081	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9838450	0.82[ASN][1000 genomes]
rs9845382	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9845542	0.82[ASN][1000 genomes]
rs9877748	0.94[EUR][1000 genomes];0.82[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	nsv876734	chr3:45725031-46468467	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer 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	42 gene(s)	inside rSNPs	diseases
2	nsv498008	chr3:45733423-46319401	Strong transcription Active TSS Genic enhancers Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2756987	chr3:46016464-46120400	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	esv2759145	chr3:46016464-46120400	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	esv1805205	chr3:46032847-46111081	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13090194	CDC25A	cis	cerebellum	SCAN
rs13090194	TDGF1	cis	parietal	SCAN
rs13090194	LIMD1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46068200-46069600	Enhancers	Placenta	Placenta
2	chr3:46068600-46069600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:46068600-46069800	ZNF genes & repeats	GM12878-XiMat	blood
4	chr3:46069000-46069600	Enhancers	H1 Cell Line	embryonic stem cell

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