Variant report

Variant	rs16861103
Chromosome Location	chr3:113233188-113233189
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 92 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs10511325	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11917149	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11917288	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11919330	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11920635	0.88[AFR][1000 genomes]
rs11920725	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11922838	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11923128	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11924109	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11926687	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13082603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs1386336	0.83[TSI][hapmap]
rs1463639	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1471883	0.94[CEU][hapmap]
rs1471884	0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1486894	0.88[MKK][hapmap];0.93[TSI][hapmap]
rs1513288	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1552433	0.95[CEU][hapmap]
rs16845109	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16860962	1.00[EUR][1000 genomes]
rs16861014	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16861023	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs16861025	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16861032	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16861045	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16861077	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16861109	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16861217	0.87[EUR][1000 genomes]
rs17255950	0.91[EUR][1000 genomes]
rs17256551	0.94[EUR][1000 genomes]
rs17256752	0.94[EUR][1000 genomes]
rs17322613	0.94[EUR][1000 genomes]
rs17325024	0.87[EUR][1000 genomes]
rs1906141	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1989359	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2087130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs2129431	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2129432	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2129434	0.83[TSI][hapmap]
rs2271496	0.87[EUR][1000 genomes]
rs2291412	0.94[EUR][1000 genomes]
rs2306068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2306070	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs2614191	0.84[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs2669909	0.95[CEU][hapmap];0.84[GIH][hapmap];0.93[MEX][hapmap];0.84[TSI][hapmap]
rs28472841	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35758075	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35812463	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4396864	1.00[CEU][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap]
rs56685963	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56772417	0.91[EUR][1000 genomes]
rs57115529	0.94[EUR][1000 genomes]
rs57164268	0.94[EUR][1000 genomes]
rs57366942	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58905600	0.94[EUR][1000 genomes]
rs58988763	0.91[EUR][1000 genomes]
rs59271111	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59493419	0.94[EUR][1000 genomes]
rs59673391	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60582065	0.84[EUR][1000 genomes]
rs60697865	0.91[EUR][1000 genomes]
rs60940543	0.94[EUR][1000 genomes]
rs61065093	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61575357	0.87[EUR][1000 genomes]
rs6438150	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438151	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6438159	0.90[MKK][hapmap];0.93[TSI][hapmap]
rs6769604	0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs6773497	0.90[TSI][hapmap]
rs6783691	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783965	0.90[TSI][hapmap]
rs6787026	0.86[TSI][hapmap]
rs6798938	0.88[MKK][hapmap];0.93[TSI][hapmap]
rs6799610	0.90[TSI][hapmap]
rs735	0.91[EUR][1000 genomes]
rs7610552	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7623919	0.94[CEU][hapmap]
rs7631335	0.88[JPT][hapmap]
rs7637618	0.90[CEU][hapmap];0.84[GIH][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap]
rs7646188	0.95[CEU][hapmap]
rs9842559	0.95[CEU][hapmap]
rs9852703	0.95[CEU][hapmap];0.84[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs9869318	0.83[TSI][hapmap]
rs9870996	0.95[CEU][hapmap]
rs9874747	0.92[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1013506	chr3:112890608-113680951	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv1004000	chr3:113116778-113513899	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv877349	chr3:113208224-113323787	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv877350	chr3:113208224-113332235	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
5	esv2050626	chr3:113233186-113233188	Active TSS Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
6	esv1027928	chr3:113233187-113233189	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs16861103	BOC	cis	parietal	SCAN
rs16861103	BOC	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:113176400-113233200	Weak transcription	Gastric	stomach
2	chr3:113184000-113233200	Weak transcription	Pancreas	Pancrea
3	chr3:113204600-113233200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:113204600-113233200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:113204600-113233200	Weak transcription	Esophagus	oesophagus
6	chr3:113204800-113233200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:113210200-113233200	Weak transcription	Colonic Mucosa	Colon
8	chr3:113225000-113233200	Weak transcription	Spleen	Spleen
9	chr3:113225200-113233200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:113225400-113233200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr3:113225400-113233200	Weak transcription	Aorta	Aorta
12	chr3:113225400-113233200	Weak transcription	Placenta	Placenta
13	chr3:113225400-113233200	Weak transcription	Left Ventricle	heart
14	chr3:113225400-113233200	Weak transcription	Ovary	ovary
15	chr3:113232000-113233400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr3:113232400-113233200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr3:113232400-113233200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr3:113232400-113233400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr3:113232400-113233400	Flanking Active TSS	Dnd41	blood
20	chr3:113232400-113235200	Active TSS	A549	lung
21	chr3:113232600-113233200	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr3:113232600-113233200	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
23	chr3:113232600-113233200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
24	chr3:113232600-113233400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr3:113232600-113233400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr3:113232600-113233400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
27	chr3:113232600-113233400	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
28	chr3:113232600-113233600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
29	chr3:113232600-113234000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:113232600-113234400	Active TSS	HMEC	breast
31	chr3:113232600-113234600	Active TSS	HUES64 Cell Line	embryonic stem cell
32	chr3:113232600-113234600	Active TSS	GM12878-XiMat	blood
33	chr3:113232600-113234600	Active TSS	K562	blood
34	chr3:113232600-113234600	Active TSS	Osteobl	bone
35	chr3:113232600-113234800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr3:113232600-113234800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:113232600-113234800	Active TSS	Right Ventricle	heart
38	chr3:113232600-113235000	Active TSS	Thymus	Thymus
39	chr3:113232600-113235000	Active TSS	NHLF	lung
40	chr3:113232800-113233200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr3:113232800-113233200	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr3:113232800-113233200	Enhancers	Primary B cells from peripheral blood	blood
43	chr3:113232800-113233200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr3:113232800-113233200	Flanking Active TSS	Colon Smooth Muscle	Colon
45	chr3:113232800-113233200	Flanking Active TSS	Duodenum Mucosa	Duodenum
46	chr3:113232800-113233200	Flanking Active TSS	Fetal Kidney	kidney
47	chr3:113232800-113233200	Flanking Active TSS	NH-A	brain
48	chr3:113232800-113233200	Flanking Active TSS	NHEK	skin
49	chr3:113232800-113233400	Flanking Active TSS	Primary T cells from cord blood	blood
50	chr3:113232800-113233400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood

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