Variant report

Variant	rs7648599
Chromosome Location	chr3:156938216-156938217
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156876962..156878616-chr3:156936583..156938253,2	K562	blood:
2	chr3:156937140..156939016-chr3:156942989..156946437,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163660	Chromatin interaction

Extended variants
information (count: 148 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:146)

rs_ID	r²[population]
rs10513508	0.91[CEU][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap]
rs10513510	0.81[GIH][hapmap]
rs10755111	0.82[CHB][hapmap]
rs10936061	0.94[EUR][1000 genomes]
rs10936062	0.94[EUR][1000 genomes]
rs10936063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs10936064	0.94[EUR][1000 genomes]
rs10936065	0.94[EUR][1000 genomes]
rs10936066	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs10936067	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10936068	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10936069	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10936074	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936075	0.86[EUR][1000 genomes]
rs10936078	0.89[CEU][hapmap]
rs10936080	0.91[CEU][hapmap]
rs10936081	0.91[CEU][hapmap]
rs1157738	0.86[CEU][hapmap];0.88[AMR][1000 genomes]
rs12488480	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12489453	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489799	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490836	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12492801	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs12496051	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12497891	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12629589	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12630209	0.94[EUR][1000 genomes]
rs12632525	0.85[ASN][1000 genomes]
rs12632562	1.00[CEU][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap]
rs12633429	1.00[CEU][hapmap];0.82[CHB][hapmap];0.81[CHD][hapmap];0.95[GIH][hapmap];0.84[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs12634818	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12635088	0.94[EUR][1000 genomes]
rs12636125	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[EUR][1000 genomes]
rs1403104	0.87[CEU][hapmap]
rs1403105	0.82[CHB][hapmap]
rs1403106	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs1403108	0.91[CEU][hapmap];0.86[CHB][hapmap];0.95[GIH][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap]
rs1500924	0.91[CEU][hapmap];0.84[JPT][hapmap]
rs1522392	0.91[CEU][hapmap];0.86[MKK][hapmap];0.97[TSI][hapmap]
rs1568611	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs16827308	0.87[CEU][hapmap]
rs16827318	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16827322	0.87[CEU][hapmap];0.87[MKK][hapmap];0.88[AMR][1000 genomes]
rs16827352	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17552941	0.94[EUR][1000 genomes]
rs1995304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2047648	0.86[CEU][hapmap]
rs2321740	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2321743	0.82[CHB][hapmap]
rs2874616	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.85[ASN][1000 genomes]
rs35910014	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3935750	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes]
rs41272613	0.94[EUR][1000 genomes]
rs4256081	0.81[AMR][1000 genomes]
rs4371471	0.93[EUR][1000 genomes]
rs4383467	0.94[EUR][1000 genomes]
rs4413278	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4608646	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs4679788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679789	0.81[EUR][1000 genomes]
rs4679790	0.82[CHB][hapmap]
rs4679791	0.82[CHB][hapmap]
rs4680340	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs4680343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680345	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4680347	0.86[CEU][hapmap];0.88[AMR][1000 genomes]
rs4680349	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4680352	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs4680353	0.82[CHB][hapmap]
rs4680354	0.90[CEU][hapmap]
rs5003893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs55828309	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55835412	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs55949516	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55953639	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56078410	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56150358	0.83[EUR][1000 genomes]
rs56263456	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57322659	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57511361	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59210914	0.92[EUR][1000 genomes]
rs59279023	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59485606	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs59865540	0.84[EUR][1000 genomes]
rs60153077	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61149035	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62274129	0.91[EUR][1000 genomes]
rs62274155	0.94[EUR][1000 genomes]
rs62274156	0.94[EUR][1000 genomes]
rs62274159	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276460	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276461	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276462	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62276465	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276470	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62276471	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276474	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62276475	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62276479	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276480	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62276488	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62276489	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62276490	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276491	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276495	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276496	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276497	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62276501	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276502	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276504	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62276505	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6441115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6441116	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[EUR][1000 genomes]
rs6441119	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6767619	0.82[CEU][hapmap]
rs6768052	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6768074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6780205	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6781682	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6788214	1.00[CEU][hapmap]
rs6792479	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6799567	0.91[CEU][hapmap];0.84[JPT][hapmap];0.97[TSI][hapmap]
rs6805989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6806232	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6809307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs73154633	0.93[EUR][1000 genomes]
rs73154649	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73154657	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154659	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73154671	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73154682	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73873800	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7610214	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7619892	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7621912	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7626589	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631257	0.91[CEU][hapmap]
rs7633004	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs7649737	0.91[CEU][hapmap];0.86[CHB][hapmap]
rs7652298	1.00[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8180056	0.94[EUR][1000 genomes]
rs8180057	0.95[EUR][1000 genomes]
rs8925	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes]
rs924516	0.87[ASN][1000 genomes]
rs949854	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[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	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
2	nsv877687	chr3:156924793-157044184	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7648599	CCNL1	cis	multi-tissue	Pritchard

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156937400-156938400	Enhancers	Osteobl	bone
2	chr3:156937800-156938800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr3:156938000-156939000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr3:156938200-156943600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr3:156938200-156948400	Weak transcription	NHDF-Ad	bronchial

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