Variant report

Variant	rs12978273
Chromosome Location	chr19:39230013-39230014
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:39229747-39230020	HepG2	liver:	n/a	n/a
2	POLR2A	chr19:39227653-39231282	PANC-1	pancreas:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:39227687..39231006-chr19:39233180..39235814,6	K562	blood:
2	chr19:39228662..39230704-chr19:39233193..39235780,3	K562	blood:
3	chr19:39228666..39232672-chr19:39336052..39337743,3	K562	blood:
4	chr19:39225398..39229275-chr19:39229442..39232488,5	K562	blood:
5	chr19:39212206..39230741-chr19:39336504..39344817,33	MCF-7	breast:
6	chr19:39228667..39230478-chr19:39420914..39423370,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ACTN4-1	chr19:39228924-39230503	ENSG00000267892.1

No data

Variant related genes	Relation type
CAPN12	TF binding region
ENSG00000269688	Chromatin interaction
ENSG00000104835	Chromatin interaction
ENSG00000128626	Chromatin interaction
ENSG00000104824	Chromatin interaction
ENSG00000182472	Chromatin interaction
ENSG00000267892	Chromatin interaction

Extended variants
information (count: 115 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs1106372	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12971309	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12972987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12972997	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12974733	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975079	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12975256	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12975953	0.96[AMR][1000 genomes]
rs12976598	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12978715	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12978914	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12979149	0.97[ASN][1000 genomes]
rs12979947	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12980399	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12980798	0.97[ASN][1000 genomes]
rs12981131	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12981984	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12983010	0.96[EUR][1000 genomes]
rs12983550	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12984794	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12985030	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12985558	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12985871	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986032	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12986121	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12986337	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17589359	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2001856	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2086148	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2126970	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2279145	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2279146	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2287728	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34026184	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34054765	1.00[AMR][1000 genomes]
rs34082501	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34105297	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs34126343	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34134906	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34305426	1.00[AMR][1000 genomes]
rs34332511	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34368672	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34525537	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34558140	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34563817	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34592527	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34695688	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34703567	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34717167	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34843929	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34862518	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34899634	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34911882	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35007285	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35074956	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35096737	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35134120	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35281901	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35403788	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35436155	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35576862	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35640008	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35666464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35685980	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35691365	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35716073	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35729716	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35807146	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35855940	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35856174	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35941349	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3786840	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs45599933	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4802774	0.86[ASN][1000 genomes]
rs56817884	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs56946356	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs57230275	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs60454376	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs61121905	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62119101	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119102	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119103	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119105	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119109	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62119116	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62120068	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62120072	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62120074	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62120085	0.89[ASN][1000 genomes]
rs62120159	0.88[AFR][1000 genomes]
rs62121819	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62121821	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62121823	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62121827	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62121828	0.81[AFR][1000 genomes]
rs62121829	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71356822	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7248577	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7260070	0.85[AFR][1000 genomes]
rs8103530	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs8104815	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105055	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105069	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105080	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105216	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8105550	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs899199	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs899200	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv817834	chr19:39174332-39237950	Enhancers Flanking Active TSS Genic enhancers Strong transcription Weak transcription Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
4	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
5	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
6	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
7	nsv911669	chr19:39196745-39231548	Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12978273	EIF3K	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:39226200-39230200	Weak transcription	NHEK	skin
2	chr19:39226200-39230600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr19:39227000-39232200	Weak transcription	Left Ventricle	heart
4	chr19:39227400-39234600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr19:39227600-39231200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
6	chr19:39228000-39231000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
7	chr19:39228000-39231000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr19:39228000-39231600	Enhancers	Primary T cells fromperipheralblood	blood
9	chr19:39228200-39230200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr19:39228200-39230400	Weak transcription	HMEC	breast
11	chr19:39228400-39230200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr19:39228400-39230400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:39228400-39230400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr19:39228400-39232400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr19:39228400-39234600	Weak transcription	Placenta	Placenta
16	chr19:39228600-39230200	Weak transcription	K562	blood
17	chr19:39228600-39230400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:39228600-39234400	Weak transcription	A549	lung
19	chr19:39228800-39230200	Weak transcription	Primary B cells from peripheral blood	blood
20	chr19:39228800-39233800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:39229000-39230800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
22	chr19:39229200-39232400	Weak transcription	Spleen	Spleen
23	chr19:39229400-39230400	Weak transcription	Esophagus	oesophagus
24	chr19:39229400-39233000	Weak transcription	HepG2	liver
25	chr19:39229600-39231000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr19:39229600-39231200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr19:39229800-39231000	Enhancers	Primary T helper naive cells from peripheral blood	blood
28	chr19:39229800-39233800	Weak transcription	Fetal Intestine Small	intestine
29	chr19:39230000-39230800	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr19:39230000-39231200	Enhancers	Primary T regulatory cells fromperipheralblood	blood

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