Variant report

Variant	rs7371503
Chromosome Location	chr2:172859611-172859612
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172856619..172859628-chr2:172864292..172866200,3	MCF-7	breast:
2	chr2:172824513..172827435-chr2:172859030..172861572,2	K562	blood:
3	chr2:172858546..172860265-chr2:172948860..172951262,2	MCF-7	breast:
4	chr2:172842087..172844341-chr2:172857534..172860058,2	K562	blood:
5	chr2:172859011..172861815-chr2:172965518..172968253,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236651	Chromatin interaction
ENSG00000115844	Chromatin interaction
ENSG00000115840	Chromatin interaction
ENSG00000144355	Chromatin interaction
ENSG00000172878	Chromatin interaction

Extended variants
information (count: 97 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs10166352	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10177679	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs10188587	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10196521	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs10439296	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930496	0.82[AMR][1000 genomes]
rs10930498	0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10930500	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10930501	0.94[ASN][1000 genomes]
rs11676484	1.00[ASW][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.85[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11677573	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11683436	0.85[ASN][1000 genomes]
rs11692418	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11695887	0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs11883977	0.84[ASN][1000 genomes]
rs11903410	0.88[ASN][1000 genomes]
rs12467010	0.90[ASN][1000 genomes]
rs12468218	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12473516	1.00[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs12478215	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12479374	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs12617265	0.88[ASW][hapmap];0.88[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12619137	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12692977	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12692979	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13017988	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13018515	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13021571	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13399316	0.88[ASW][hapmap];0.94[CHD][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs1400816	1.00[JPT][hapmap]
rs1443699	0.88[ASN][1000 genomes]
rs1443700	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1878583	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs1982288	0.87[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2028670	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2028671	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2028672	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2056202	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2138873	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2176466	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2357064	0.89[CEU][hapmap];1.00[JPT][hapmap]
rs2357206	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2357207	0.90[ASN][1000 genomes]
rs2357208	1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28372952	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2884123	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3770443	1.00[JPT][hapmap]
rs3770453	0.89[CEU][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs3791343	0.94[ASN][1000 genomes]
rs3821092	1.00[JPT][hapmap]
rs3821094	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs3821096	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4072279	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4324292	1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4668413	0.87[EUR][1000 genomes]
rs4668415	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4668416	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4668417	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4668419	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs59853867	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs60315614	0.81[AMR][1000 genomes]
rs60706248	0.90[ASN][1000 genomes]
rs6433315	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6433317	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6433318	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs6433321	0.80[LWK][hapmap];0.80[YRI][hapmap]
rs6433322	0.94[ASW][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.88[JPT][hapmap];0.83[YRI][hapmap];0.88[ASN][1000 genomes]
rs6707142	0.88[ASW][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6708365	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6711813	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6714214	0.88[ASW][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs6726991	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6727459	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6733123	0.88[ASN][1000 genomes]
rs6736159	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6740705	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6742905	0.90[ASN][1000 genomes]
rs6753859	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs6757680	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6758494	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6760680	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7340516	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7371631	0.88[ASN][1000 genomes]
rs7579509	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7580132	0.88[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7580232	0.88[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7588025	0.83[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7594478	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7597525	0.90[ASN][1000 genomes]
rs7598232	0.85[ASN][1000 genomes]
rs925881	0.88[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9636293	0.87[EUR][1000 genomes]
rs970948	0.94[ASW][hapmap];0.89[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]

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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
4	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7371503	RAPGEF4	cis	cerebellum	SCAN
rs7371503	METTL8	cis	multi-tissue	Pritchard
rs7371503	MAP1D	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172810000-172862600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172821000-172862800	Weak transcription	Brain Angular Gyrus	brain
3	chr2:172847400-172864000	Weak transcription	HSMM	muscle
4	chr2:172848000-172863200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr2:172849600-172863800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:172850400-172860600	Weak transcription	Primary hematopoietic stem cells	blood
7	chr2:172856600-172863200	Weak transcription	K562	blood
8	chr2:172858000-172860400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:172858200-172860000	Enhancers	Brain Germinal Matrix	brain
10	chr2:172858600-172863200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr2:172859400-172863600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:172859600-172860400	Enhancers	Ovary	ovary

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