Variant report

Variant	rs12495460
Chromosome Location	chr3:67501115-67501116
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67498464..67501413-chr3:67503941..67505935,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11127623	0.86[ASN][1000 genomes]
rs11710800	0.92[ASN][1000 genomes]
rs11920877	0.86[ASN][1000 genomes]
rs11923553	0.86[ASN][1000 genomes]
rs12374036	0.91[ASN][1000 genomes]
rs12497043	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13059103	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13076634	0.92[ASN][1000 genomes]
rs13090999	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13095360	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4327406	0.81[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs4577484	0.90[ASN][1000 genomes]
rs4645146	0.90[ASN][1000 genomes]
rs4856782	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4856863	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4856864	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4856865	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55887942	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60806282	0.87[ASN][1000 genomes]
rs60931405	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62256379	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs62256386	0.92[ASN][1000 genomes]
rs62256387	0.92[ASN][1000 genomes]
rs62256391	0.87[ASN][1000 genomes]
rs62256392	0.87[ASN][1000 genomes]
rs6767651	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6768043	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6769758	0.92[ASN][1000 genomes]
rs6770533	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6773365	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6773425	0.92[ASN][1000 genomes]
rs6779086	0.80[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs6780361	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6791455	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6810165	0.92[ASN][1000 genomes]
rs7614213	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620241	0.91[ASN][1000 genomes]
rs7635366	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][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	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
6	nsv508221	chr3:67487240-67509429	Weak transcription Enhancers Strong transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv3860	chr3:67493286-67517941	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12495460	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67435600-67509800	Weak transcription	Ovary	ovary
2	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
3	chr3:67466600-67508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:67471200-67503800	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr3:67472000-67506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr3:67472000-67509800	Weak transcription	HSMM	muscle
8	chr3:67473400-67521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:67478200-67512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr3:67482600-67527200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr3:67482600-67528600	Weak transcription	GM12878-XiMat	blood
13	chr3:67482800-67503800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:67482800-67520800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr3:67482800-67533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:67484000-67511400	Weak transcription	Fetal Lung	lung
17	chr3:67485800-67503800	Weak transcription	Primary B cells from cord blood	blood
18	chr3:67486800-67506000	Weak transcription	Primary T cells from cord blood	blood
19	chr3:67487000-67518600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:67487800-67503400	Weak transcription	Liver	Liver
21	chr3:67487800-67512200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:67488000-67544200	Weak transcription	A549	lung
23	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr3:67490200-67511800	Weak transcription	HSMMtube	muscle
25	chr3:67492200-67545400	Weak transcription	Fetal Intestine Small	intestine
26	chr3:67492400-67515400	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:67492400-67516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr3:67498000-67534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:67499400-67512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:67500600-67504400	Weak transcription	HepG2	liver
31	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea

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