Variant report

Variant	rs16957250
Chromosome Location	chr15:43170823-43170824
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	chr15:43169823..43171405-chr15:43172916..43175738,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10467975	1.00[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap]
rs11070380	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs11070382	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11070386	1.00[CEU][hapmap]
rs11630595	1.00[CEU][hapmap]
rs11853250	0.88[CEU][hapmap];0.92[GIH][hapmap];0.92[JPT][hapmap]
rs12441352	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1381856	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1462856	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap]
rs16957165	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs16957167	1.00[CEU][hapmap]
rs16957244	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];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16957385	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs1972447	0.85[EUR][1000 genomes]
rs1993813	0.84[EUR][1000 genomes]
rs2054389	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2126602	0.82[EUR][1000 genomes]
rs2412746	0.84[EUR][1000 genomes]
rs2412747	0.84[EUR][1000 genomes]
rs2682073	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]
rs2733224	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2899069	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3736054	0.82[MEX][hapmap]
rs3803341	1.00[CEU][hapmap];0.94[MEX][hapmap];0.86[EUR][1000 genomes]
rs4244590	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4338775	0.84[EUR][1000 genomes]
rs4509988	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4573908	1.00[CEU][hapmap]
rs4923955	1.00[CEU][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes]
rs4924701	0.83[EUR][1000 genomes]
rs4924704	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs55805543	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60763334	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6416436	0.84[EUR][1000 genomes]
rs6493065	0.86[GIH][hapmap]
rs6493071	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493076	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap]
rs6493077	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs66530524	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7162939	0.93[EUR][1000 genomes]
rs7162959	0.90[EUR][1000 genomes]
rs7174028	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.85[TSI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7178567	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8027733	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs8031767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8037022	1.00[CEU][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes]
rs8042481	1.00[CEU][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes]
rs9920498	0.87[EUR][1000 genomes]

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
rs16957250	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs16957250	TGM5	cis	lymphoblastoid	seeQTL
rs16957250	TTBK2	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

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	chr15:43119600-43172600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:43125400-43173600	Weak transcription	Hela-S3	cervix
5	chr15:43131600-43171800	Weak transcription	Brain Anterior Caudate	brain
6	chr15:43132000-43186800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr15:43132400-43172800	Weak transcription	Ovary	ovary
8	chr15:43132600-43171200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr15:43136800-43182400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr15:43142400-43182400	Weak transcription	Lung	lung
11	chr15:43142800-43172000	Weak transcription	Fetal Intestine Large	intestine
12	chr15:43151600-43182400	Weak transcription	Aorta	Aorta
13	chr15:43151800-43173000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:43151800-43178600	Weak transcription	Placenta	Placenta
15	chr15:43154200-43174000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:43154600-43182400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:43155000-43182600	Weak transcription	Primary T cells from cord blood	blood
18	chr15:43156000-43171400	Weak transcription	Fetal Brain Male	brain
19	chr15:43156000-43172400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:43156000-43172800	Weak transcription	Brain Cingulate Gyrus	brain
21	chr15:43156800-43172000	Weak transcription	Gastric	stomach
22	chr15:43157600-43171600	Weak transcription	Liver	Liver
23	chr15:43158000-43172000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:43158000-43172600	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr15:43158400-43172600	Weak transcription	Monocytes-CD14+_RO01746	blood
26	chr15:43159400-43171800	Weak transcription	Brain Substantia Nigra	brain
27	chr15:43163400-43172600	Weak transcription	Left Ventricle	heart
28	chr15:43163400-43176800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr15:43163800-43172000	Weak transcription	Esophagus	oesophagus
30	chr15:43164000-43172600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:43166200-43175000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:43170600-43171000	Strong transcription	Primary B cells from cord blood	blood
33	chr15:43170600-43171000	Enhancers	K562	blood

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