Variant report

Variant	rs16957165
Chromosome Location	chr15:43084892-43084893
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10467975	0.81[ASW][hapmap];1.00[CEU][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.92[TSI][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11070377	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs11070380	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11070382	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap]
rs11632809	0.86[ASN][1000 genomes]
rs11853250	0.88[CEU][hapmap];0.92[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11854550	0.94[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11854668	0.94[EUR][1000 genomes]
rs12591415	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs12592573	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs12594600	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs12594696	0.81[ASW][hapmap];0.85[YRI][hapmap]
rs12594765	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs16957055	0.81[YRI][hapmap]
rs16957063	0.81[YRI][hapmap]
rs16957120	0.85[YRI][hapmap]
rs16957167	1.00[CEU][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16957244	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]
rs16957250	1.00[CEU][hapmap];0.85[JPT][hapmap]
rs16957264	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs2682073	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]
rs34302400	0.86[ASN][1000 genomes]
rs35554267	0.91[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs3742992	0.81[YRI][hapmap]
rs3742995	0.81[YRI][hapmap]
rs3803341	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap]
rs4334272	0.81[ASW][hapmap]
rs55927779	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493065	0.94[MKK][hapmap];0.85[YRI][hapmap]
rs66530524	0.90[ASN][1000 genomes]
rs67920450	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7174028	0.81[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap];0.81[LWK][hapmap]
rs7178567	1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs7181238	0.87[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.84[ASN][1000 genomes]
rs8028699	0.85[YRI][hapmap]
rs8031767	0.81[ASW][hapmap];1.00[CEU][hapmap];0.85[JPT][hapmap];0.81[LWK][hapmap];0.81[YRI][hapmap]
rs8033336	0.87[ASW][hapmap];0.90[YRI][hapmap]
rs8037022	1.00[CEU][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap]
rs8042980	0.84[ASN][1000 genomes]
rs9920092	0.93[CHB][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9920562	0.80[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MKK][hapmap];0.90[YRI][hapmap];0.86[ASN][1000 genomes]
rs9920624	0.93[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9920935	0.94[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.94[MKK][hapmap];0.81[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16957165	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs16957165	CCNDBP1	cis	multi-tissue	Pritchard
rs16957165	ELL3	cis	lymphoblastoid	seeQTL
rs16957165	TGM5	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43030000-43093600	Weak transcription	Colonic Mucosa	Colon
2	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr15:43056800-43116800	Weak transcription	HepG2	liver
5	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
7	chr15:43062600-43087800	Weak transcription	K562	blood
8	chr15:43062800-43088600	Weak transcription	NHDF-Ad	bronchial
9	chr15:43063000-43093000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:43063400-43093600	Weak transcription	Esophagus	oesophagus
11	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
12	chr15:43064000-43114200	Weak transcription	Fetal Kidney	kidney
13	chr15:43064800-43150800	Weak transcription	HSMM	muscle
14	chr15:43066400-43095600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr15:43066600-43088600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr15:43066600-43097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr15:43067600-43092800	Weak transcription	Brain Germinal Matrix	brain
19	chr15:43067800-43093000	Weak transcription	Fetal Brain Female	brain
20	chr15:43067800-43095200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr15:43068000-43093000	Weak transcription	Spleen	Spleen
22	chr15:43068400-43089200	Weak transcription	HUVEC	blood vessel
23	chr15:43068400-43093000	Weak transcription	Aorta	Aorta
24	chr15:43068400-43093600	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:43068800-43089600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:43068800-43092600	Weak transcription	Brain Hippocampus Middle	brain
27	chr15:43069000-43086400	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr15:43069000-43092800	Weak transcription	Fetal Muscle Trunk	muscle
29	chr15:43069000-43093400	Weak transcription	Duodenum Mucosa	Duodenum
30	chr15:43075200-43092600	Weak transcription	Fetal Heart	heart
31	chr15:43075200-43093600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr15:43075200-43143800	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr15:43075400-43135800	Weak transcription	HSMMtube	muscle
34	chr15:43075600-43085000	Weak transcription	Brain Angular Gyrus	brain
35	chr15:43075600-43086400	Weak transcription	Brain Anterior Caudate	brain
36	chr15:43075600-43086400	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr15:43075600-43088600	Weak transcription	NHEK	skin
38	chr15:43075600-43093000	Weak transcription	Brain Cingulate Gyrus	brain
39	chr15:43075600-43093400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr15:43075600-43093600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr15:43075600-43093600	Weak transcription	Fetal Lung	lung
42	chr15:43075600-43093600	Weak transcription	Rectal Mucosa Donor 29	rectum
43	chr15:43075600-43150800	Weak transcription	Colon Smooth Muscle	Colon
44	chr15:43075800-43085000	Weak transcription	Dnd41	blood
45	chr15:43075800-43085200	Weak transcription	Adipose Nuclei	Adipose
46	chr15:43075800-43085200	Weak transcription	Fetal Intestine Large	intestine
47	chr15:43075800-43085400	Weak transcription	Liver	Liver
48	chr15:43075800-43088200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr15:43075800-43088200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr15:43075800-43088400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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