Variant report

Variant	rs9920935
Chromosome Location	chr15:43075202-43075203
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10467975	0.86[ASW][hapmap];0.86[LWK][hapmap];1.00[MKK][hapmap];0.85[YRI][hapmap]
rs11070377	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11070378	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070380	0.94[CHB][hapmap];0.81[ASN][1000 genomes]
rs11070382	0.86[ASW][hapmap];0.84[CHD][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap]
rs11632809	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11853250	0.86[LWK][hapmap];0.97[MKK][hapmap]
rs11854550	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12323990	0.94[LWK][hapmap];0.84[YRI][hapmap]
rs12591415	0.86[ASW][hapmap];0.81[LWK][hapmap];0.84[YRI][hapmap]
rs12592573	0.86[LWK][hapmap];0.90[YRI][hapmap]
rs12594600	0.86[ASW][hapmap];0.95[YRI][hapmap];0.86[AFR][1000 genomes]
rs12594696	0.86[ASW][hapmap];0.86[LWK][hapmap];0.84[YRI][hapmap]
rs12594699	0.88[AFR][1000 genomes]
rs12594724	0.82[AFR][1000 genomes]
rs12594765	0.83[LWK][hapmap];0.90[YRI][hapmap]
rs16957031	0.85[YRI][hapmap]
rs16957037	0.94[LWK][hapmap];0.84[YRI][hapmap]
rs16957055	0.94[LWK][hapmap];0.90[YRI][hapmap]
rs16957061	0.91[LWK][hapmap];0.83[YRI][hapmap]
rs16957063	0.97[LWK][hapmap];0.90[YRI][hapmap]
rs16957120	0.85[YRI][hapmap]
rs16957165	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]
rs16957244	0.85[ASW][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap]
rs2139655	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs2682073	0.94[CHB][hapmap];1.00[CHD][hapmap]
rs28437884	0.80[AFR][1000 genomes]
rs28542286	0.87[AFR][1000 genomes]
rs28722903	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34302400	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35554267	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3742992	0.90[YRI][hapmap]
rs3742995	0.97[LWK][hapmap];0.90[YRI][hapmap]
rs4334272	0.86[ASW][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs4924696	0.92[CEU][hapmap]
rs55927779	0.83[ASN][1000 genomes]
rs58548142	0.80[AFR][1000 genomes]
rs6493065	0.93[ASW][hapmap];1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs67920450	0.82[ASN][1000 genomes]
rs7174028	0.86[ASW][hapmap];0.84[CHD][hapmap];0.86[LWK][hapmap]
rs7178567	0.80[ASW][hapmap];0.82[CHB][hapmap]
rs7181238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.86[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8024266	1.00[CEU][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8028167	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8028699	0.90[YRI][hapmap]
rs8030696	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8031767	0.86[ASW][hapmap];0.86[LWK][hapmap];0.81[YRI][hapmap]
rs8033336	0.86[LWK][hapmap];0.90[YRI][hapmap]
rs8042738	0.86[EUR][1000 genomes]
rs8042980	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920092	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9920562	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920624	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9920935	CCNDBP1	cis	multi-tissue	Pritchard
rs9920935	TGM5	cis	multi-tissue	Pritchard

Chromatin state (count:109 , 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	chr15:43051800-43083800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr15:43053600-43112200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:43054000-43080200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr15:43054800-43146000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr15:43056800-43116800	Weak transcription	HepG2	liver
7	chr15:43057600-43107000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr15:43060800-43122200	Weak transcription	GM12878-XiMat	blood
9	chr15:43062600-43087800	Weak transcription	K562	blood
10	chr15:43062800-43088600	Weak transcription	NHDF-Ad	bronchial
11	chr15:43063000-43083200	Weak transcription	Fetal Intestine Small	intestine
12	chr15:43063000-43093000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr15:43063400-43093600	Weak transcription	Esophagus	oesophagus
14	chr15:43063400-43136200	Weak transcription	Psoas Muscle	Psoas
15	chr15:43064000-43114200	Weak transcription	Fetal Kidney	kidney
16	chr15:43064800-43150800	Weak transcription	HSMM	muscle
17	chr15:43066400-43095600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:43066600-43088600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:43066600-43097600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr15:43067400-43147200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
21	chr15:43067600-43078400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr15:43067600-43092800	Weak transcription	Brain Germinal Matrix	brain
23	chr15:43067800-43093000	Weak transcription	Fetal Brain Female	brain
24	chr15:43067800-43095200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr15:43068000-43077800	Weak transcription	HMEC	breast
26	chr15:43068000-43093000	Weak transcription	Spleen	Spleen
27	chr15:43068400-43089200	Weak transcription	HUVEC	blood vessel
28	chr15:43068400-43093000	Weak transcription	Aorta	Aorta
29	chr15:43068400-43093600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr15:43068800-43077000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:43068800-43089600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr15:43068800-43092600	Weak transcription	Brain Hippocampus Middle	brain
33	chr15:43069000-43076800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:43069000-43079200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr15:43069000-43086400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:43069000-43092800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:43069000-43093400	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:43069400-43075400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:43072600-43078200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr15:43073000-43076000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:43073200-43075800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:43073200-43076200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr15:43073400-43076000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr15:43073400-43078400	Weak transcription	NH-A	brain
45	chr15:43073600-43075800	Strong transcription	Primary neutrophils fromperipheralblood	blood
46	chr15:43074000-43075800	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr15:43074200-43075800	Strong transcription	Placenta	Placenta
48	chr15:43074200-43076600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr15:43074400-43075600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr15:43074400-43075800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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