Variant report

Variant	rs2682073
Chromosome Location	chr15:43196558-43196559
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	chr15:43196236..43198232-chr15:43199329..43201446,2	K562	blood:

Variant related genes	Relation type
ENSG00000128881	Chromatin interaction

Extended variants
information (count: 83 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1037990	0.85[EUR][1000 genomes]
rs10467975	0.93[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.90[YRI][hapmap]
rs11070380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.89[ASN][1000 genomes]
rs11070382	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11070386	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs11070387	0.83[EUR][1000 genomes]
rs11630595	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs11853250	0.86[ASW][hapmap];0.88[CEU][hapmap];0.92[JPT][hapmap];0.90[LWK][hapmap];0.81[YRI][hapmap]
rs11854550	0.94[CHB][hapmap];0.80[YRI][hapmap]
rs12050596	0.84[EUR][1000 genomes]
rs12441352	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12591415	0.93[ASW][hapmap];0.81[YRI][hapmap]
rs12592573	1.00[ASW][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap]
rs12594600	0.93[ASW][hapmap];0.81[YRI][hapmap]
rs12594696	0.93[ASW][hapmap];0.85[LWK][hapmap];0.81[YRI][hapmap]
rs12594765	1.00[ASW][hapmap];0.82[LWK][hapmap];0.86[YRI][hapmap]
rs12913617	0.83[EUR][1000 genomes]
rs1381856	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1462856	0.86[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs16957120	0.81[YRI][hapmap]
rs16957165	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.86[YRI][hapmap];0.86[ASN][1000 genomes]
rs16957167	1.00[CEU][hapmap]
rs16957244	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16957250	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957264	0.88[CEU][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1972447	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1993813	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2035170	0.83[EUR][1000 genomes]
rs2054389	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2126602	0.84[EUR][1000 genomes]
rs2412746	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412747	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2412752	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2733224	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899069	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736054	0.86[ASW][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap]
rs3784265	0.83[EUR][1000 genomes]
rs3803341	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4244590	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4338775	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4509988	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4573908	1.00[CEU][hapmap];0.86[JPT][hapmap];0.83[EUR][1000 genomes]
rs4923955	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924701	0.89[EUR][1000 genomes]
rs4924704	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs55805543	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55927779	0.84[ASN][1000 genomes]
rs60763334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6416436	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493065	0.86[ASW][hapmap];0.81[YRI][hapmap]
rs6493071	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493076	0.86[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes]
rs6493077	1.00[CEU][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs66530524	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67920450	0.90[ASN][1000 genomes]
rs7162939	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7162959	0.96[EUR][1000 genomes]
rs7174028	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178567	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7181238	1.00[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap]
rs8027733	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs8031767	0.93[ASW][hapmap];1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8033336	1.00[ASW][hapmap];0.85[LWK][hapmap];0.86[YRI][hapmap]
rs8037022	1.00[CEU][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs8042481	1.00[CEU][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs9920092	0.93[CHB][hapmap];0.80[YRI][hapmap]
rs9920498	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9920562	0.93[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.87[LWK][hapmap];0.86[YRI][hapmap]
rs9920624	0.81[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[YRI][hapmap]
rs9920904	0.83[EUR][1000 genomes]
rs9920935	0.94[CHB][hapmap];1.00[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' 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
2	nsv1050128	chr15:43056145-43262736	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv542368	chr15:43056145-43262736	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
5	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
8	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3408090	chr15:43172709-43207571	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv3366604	chr15:43172709-43210677	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3408604	chr15:43175709-43207571	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2682073	TGM5	cis	lymphoblastoid	seeQTL
rs2682073	CCNDBP1	cis	multi-tissue	Pritchard
rs2682073	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs2682073	ELL3	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43182800-43207000	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr15:43183200-43211600	Weak transcription	Left Ventricle	heart
3	chr15:43183600-43201400	Weak transcription	Lung	lung
4	chr15:43183800-43207200	Weak transcription	Ovary	ovary
5	chr15:43184200-43203400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr15:43184200-43207400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:43185600-43207000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:43187000-43200400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:43187000-43207600	Weak transcription	Primary B cells from cord blood	blood
10	chr15:43187000-43211600	Weak transcription	Fetal Muscle Leg	muscle
11	chr15:43187200-43199800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:43187200-43210600	Weak transcription	Primary T cells from cord blood	blood
13	chr15:43187400-43200400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:43187400-43206600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:43189200-43211600	Weak transcription	Fetal Intestine Small	intestine
16	chr15:43190600-43197600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr15:43196000-43201400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:43196000-43211600	Weak transcription	Small Intestine	intestine
19	chr15:43196200-43196600	Enhancers	GM12878-XiMat	blood
20	chr15:43196200-43205400	Weak transcription	Monocytes-CD14+_RO01746	blood
21	chr15:43196200-43206200	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr15:43196200-43207000	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:43196200-43211400	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:43196400-43197000	Enhancers	Fetal Heart	heart
25	chr15:43196400-43200800	Weak transcription	K562	blood
26	chr15:43196400-43203000	Weak transcription	Psoas Muscle	Psoas
27	chr15:43196400-43203400	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:43196400-43207000	Weak transcription	Brain Hippocampus Middle	brain
29	chr15:43196400-43207400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
30	chr15:43196400-43211600	Weak transcription	Right Atrium	heart
31	chr15:43196400-43211600	Weak transcription	Right Ventricle	heart

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