Variant report

Variant	rs12972997
Chromosome Location	chr19:39238229-39238230
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:39236154..39238526-chr19:39239272..39240879,2	K562	blood:
2	chr19:39236132..39238637-chr19:39263161..39265778,2	K562	blood:
3	chr19:39236238..39239622-chr19:39320803..39323226,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000104823	Chromatin interaction
ENSG00000205076	Chromatin interaction

Extended variants
information (count: 151 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1106372	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11083478	0.96[ASN][1000 genomes]
rs12971309	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12972987	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12974733	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12975079	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12975256	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12975953	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes]
rs12976598	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12977599	0.80[AFR][1000 genomes]
rs12977631	1.00[ASN][1000 genomes]
rs12978273	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12978715	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12978914	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12979947	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12980399	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12981131	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12981984	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12983010	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12983550	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12984794	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12985030	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12985558	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12985871	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12986032	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12986121	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12986337	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17589359	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2001856	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2086147	0.89[ASN][1000 genomes]
rs2086148	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2100941	0.96[ASN][1000 genomes]
rs2126970	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2279145	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2279146	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2287728	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2368524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34026184	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34054765	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34082501	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34090445	1.00[ASN][1000 genomes]
rs34105297	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34126343	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34134906	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34305426	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34332511	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34361849	0.81[ASN][1000 genomes]
rs34368672	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34525537	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34558140	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34563817	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34592527	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34695688	0.84[AMR][1000 genomes]
rs34703567	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34717167	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34776027	0.96[ASN][1000 genomes]
rs34834035	0.96[ASN][1000 genomes]
rs34843929	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34862518	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34899634	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34911882	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35007285	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35026669	0.93[ASN][1000 genomes]
rs35074956	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35096737	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35134120	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs35193699	0.81[AFR][1000 genomes]
rs35253157	0.87[ASN][1000 genomes]
rs35281901	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35335944	0.96[ASN][1000 genomes]
rs35403788	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35436155	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35502825	0.96[ASN][1000 genomes]
rs35576862	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35604174	0.96[ASN][1000 genomes]
rs35640008	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35666464	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35685980	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35691365	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs35716073	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35729716	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35807146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35855940	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35856174	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35941349	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35974114	0.93[ASN][1000 genomes]
rs3786840	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4435378	0.96[ASN][1000 genomes]
rs4473308	0.96[ASN][1000 genomes]
rs4474812	0.96[ASN][1000 genomes]
rs4491650	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs45599933	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4801868	0.96[ASN][1000 genomes]
rs4802795	0.96[ASN][1000 genomes]
rs4802796	0.96[ASN][1000 genomes]
rs56817884	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56946356	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57230275	0.95[AMR][1000 genomes]
rs58794115	0.85[ASN][1000 genomes]
rs59073128	0.96[ASN][1000 genomes]
rs60454376	0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs61121905	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61417362	0.93[ASN][1000 genomes]
rs62119101	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119102	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119103	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119109	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62119116	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62120068	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62120072	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62120074	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62120091	1.00[ASN][1000 genomes]
rs62120094	1.00[ASN][1000 genomes]
rs62120159	0.92[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62121365	0.93[ASN][1000 genomes]
rs62121373	0.96[ASN][1000 genomes]
rs62121374	0.96[ASN][1000 genomes]
rs62121375	0.96[ASN][1000 genomes]
rs62121763	0.80[AFR][1000 genomes]
rs62121819	0.84[AMR][1000 genomes]
rs62121821	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62121823	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62121827	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs62121828	0.84[AFR][1000 genomes]
rs62121829	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71356822	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7246368	0.80[AFR][1000 genomes]
rs7248577	1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7253700	0.96[ASN][1000 genomes]
rs7257060	0.89[ASN][1000 genomes]
rs7257063	0.89[ASN][1000 genomes]
rs7260070	0.88[AFR][1000 genomes]
rs732135	0.85[CEU][hapmap]
rs73554745	0.96[ASN][1000 genomes]
rs7508528	0.96[ASN][1000 genomes]
rs8103530	0.84[AMR][1000 genomes]
rs8104815	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8105055	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8105069	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8105080	1.00[CEU][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8105216	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8105550	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs899199	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs899200	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs973009	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv833828	chr19:39084759-39257979	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1057899	chr19:39088319-39475493	Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
3	nsv911668	chr19:39174669-39291771	Genic enhancers Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	esv1826260	chr19:39178364-39248836	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS 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 miRNA target site	12 gene(s)	inside rSNPs	diseases
5	esv1837023	chr19:39190588-39425722	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12972997	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39235200-39244400	Weak transcription	HepG2	liver
2	chr19:39236000-39240800	Weak transcription	K562	blood
3	chr19:39236600-39245600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

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