Variant report

Variant	rs16957244
Chromosome Location	chr15:43166029-43166030
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1037990	0.85[EUR][1000 genomes]
rs10467975	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.95[YRI][hapmap]
rs11070380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs11070382	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][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	0.92[ASW][hapmap];0.88[CEU][hapmap];0.92[JPT][hapmap];1.00[LWK][hapmap];0.86[YRI][hapmap]
rs11854550	0.94[CHB][hapmap]
rs12050596	0.84[EUR][1000 genomes]
rs12323990	0.84[ASW][hapmap];0.81[LWK][hapmap]
rs12441352	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12591415	1.00[ASW][hapmap]
rs12592573	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs12594600	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs12594696	1.00[ASW][hapmap]
rs12594765	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs12913617	0.83[EUR][1000 genomes]
rs1381856	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1462856	0.92[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.81[EUR][1000 genomes]
rs16957037	0.84[ASW][hapmap];0.81[LWK][hapmap]
rs16957055	0.92[ASW][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap]
rs16957061	0.92[ASW][hapmap]
rs16957063	0.92[ASW][hapmap];0.84[LWK][hapmap];0.81[YRI][hapmap]
rs16957165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap];0.92[ASN][1000 genomes]
rs16957167	1.00[CEU][hapmap]
rs16957250	1.00[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16957264	0.88[CEU][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1972447	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1993813	0.90[EUR][1000 genomes]
rs2035170	0.83[EUR][1000 genomes]
rs2054389	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2126602	0.84[EUR][1000 genomes]
rs2412746	0.90[EUR][1000 genomes]
rs2412747	0.90[EUR][1000 genomes]
rs2412752	0.86[JPT][hapmap];0.83[MEX][hapmap]
rs2682073	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]
rs2733224	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2899069	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3736054	0.92[ASW][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.88[MEX][hapmap];0.86[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap]
rs3742992	0.81[YRI][hapmap]
rs3742995	0.92[ASW][hapmap];0.84[LWK][hapmap];0.81[YRI][hapmap]
rs3784265	0.83[EUR][1000 genomes]
rs3803341	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4244590	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4334272	1.00[ASW][hapmap]
rs4338775	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4509988	0.88[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];0.86[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4924701	0.89[EUR][1000 genomes]
rs4924704	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs55805543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs55927779	0.90[ASN][1000 genomes]
rs60763334	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6416436	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493065	0.92[ASW][hapmap];0.86[LWK][hapmap];0.85[YRI][hapmap]
rs6493071	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6493076	0.92[ASW][hapmap];1.00[CEU][hapmap];0.81[CHB][hapmap];0.84[GIH][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.84[EUR][1000 genomes]
rs6493077	1.00[CEU][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs66530524	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67920450	0.96[ASN][1000 genomes]
rs7162939	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7162959	0.96[EUR][1000 genomes]
rs7174028	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178567	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7181238	0.92[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[YRI][hapmap]
rs8027733	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs8028699	0.85[YRI][hapmap]
rs8031767	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8033336	0.92[ASW][hapmap];0.81[YRI][hapmap]
rs8037022	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs8042481	1.00[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs9920092	0.93[CHB][hapmap]
rs9920498	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9920562	0.85[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.81[YRI][hapmap]
rs9920624	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs9920904	0.83[EUR][1000 genomes]
rs9920935	0.85[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.81[YRI][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	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	esv3490431	chr15:43148709-43190630	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv3490432	chr15:43148709-43190630	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
12	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16957244	CCNDBP1	cis	multi-tissue	Pritchard
rs16957244	ELL3	cis	lymphoblastoid	seeQTL
rs16957244	TGM5	cis	lymphoblastoid	seeQTL

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43103400-43173200	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:43114800-43172000	Weak transcription	Pancreas	Pancrea
3	chr15:43119600-43168200	Weak transcription	Stomach Smooth Muscle	stomach
4	chr15:43119600-43172600	Weak transcription	Brain Inferior Temporal Lobe	brain
5	chr15:43119800-43170200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr15:43125400-43173600	Weak transcription	Hela-S3	cervix
7	chr15:43131600-43171800	Weak transcription	Brain Anterior Caudate	brain
8	chr15:43132000-43186800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:43132200-43166200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr15:43132400-43172800	Weak transcription	Ovary	ovary
11	chr15:43132600-43171200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:43136600-43167200	Weak transcription	Dnd41	blood
13	chr15:43136800-43169200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr15:43136800-43169200	Weak transcription	Fetal Intestine Small	intestine
15	chr15:43136800-43182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:43142400-43182400	Weak transcription	Lung	lung
17	chr15:43142600-43169400	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr15:43142600-43170200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:43142800-43172000	Weak transcription	Fetal Intestine Large	intestine
20	chr15:43145400-43169200	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:43151000-43169400	Weak transcription	Rectal Smooth Muscle	rectum
22	chr15:43151600-43182400	Weak transcription	Aorta	Aorta
23	chr15:43151800-43169200	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:43151800-43173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:43151800-43178600	Weak transcription	Placenta	Placenta
26	chr15:43152200-43167400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr15:43152200-43170000	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr15:43154200-43174000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr15:43154600-43182400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr15:43155000-43182600	Weak transcription	Primary T cells from cord blood	blood
31	chr15:43156000-43171400	Weak transcription	Fetal Brain Male	brain
32	chr15:43156000-43172400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr15:43156000-43172800	Weak transcription	Brain Cingulate Gyrus	brain
34	chr15:43156800-43172000	Weak transcription	Gastric	stomach
35	chr15:43157600-43171600	Weak transcription	Liver	Liver
36	chr15:43158000-43169400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:43158000-43172000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr15:43158000-43172600	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr15:43158400-43172600	Weak transcription	Monocytes-CD14+_RO01746	blood
40	chr15:43159400-43171800	Weak transcription	Brain Substantia Nigra	brain
41	chr15:43160400-43167400	Weak transcription	Primary B cells from cord blood	blood
42	chr15:43161600-43169600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:43162400-43168200	Weak transcription	Right Ventricle	heart
44	chr15:43163400-43172600	Weak transcription	Left Ventricle	heart
45	chr15:43163400-43176800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:43163800-43167200	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr15:43163800-43172000	Weak transcription	Esophagus	oesophagus
48	chr15:43164000-43172600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr15:43164200-43169600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:43165800-43166200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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