Variant report

Variant	rs16863204
Chromosome Location	chr3:150889879-150889880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10513385	0.83[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10513386	0.80[CHD][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11713719	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs11714357	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs12106682	1.00[ASW][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs12631155	0.89[ASW][hapmap]
rs12636713	0.85[YRI][hapmap];1.00[EUR][1000 genomes]
rs1431494	0.89[ASW][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1431495	0.83[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1431496	0.89[YRI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863149	0.82[CHB][hapmap];0.91[JPT][hapmap];1.00[TSI][hapmap]
rs16863153	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs16863155	0.83[EUR][1000 genomes]
rs16863161	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs16863203	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs16863208	0.86[CHD][hapmap];1.00[MEX][hapmap];0.88[YRI][hapmap];0.83[EUR][1000 genomes]
rs16863219	1.00[ASW][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs16863223	0.83[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863227	0.82[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863229	0.89[ASW][hapmap];0.80[CHD][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16863238	0.80[CHD][hapmap];1.00[TSI][hapmap]
rs16863239	1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs16863248	0.89[ASW][hapmap]
rs2043170	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2870413	0.89[ASW][hapmap]
rs2870415	0.89[ASW][hapmap]
rs3732755	1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs3732756	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs3773614	0.89[ASW][hapmap]
rs41526246	0.89[ASW][hapmap]
rs41526349	1.00[ASW][hapmap];0.83[YRI][hapmap];0.89[AFR][1000 genomes]
rs4330297	0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56151283	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56350229	1.00[EUR][1000 genomes]
rs59669423	1.00[EUR][1000 genomes]
rs60620665	0.87[AFR][1000 genomes]
rs60749276	1.00[EUR][1000 genomes]
rs60966250	0.89[AFR][1000 genomes]
rs61099669	1.00[EUR][1000 genomes]
rs6440723	0.89[ASW][hapmap]
rs6772538	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6772543	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6775269	1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6794447	0.81[AFR][1000 genomes]
rs6802229	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73016712	0.87[AFR][1000 genomes]
rs73016789	0.89[AFR][1000 genomes]
rs73016801	0.83[EUR][1000 genomes]
rs73018604	1.00[EUR][1000 genomes]
rs73018614	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018620	0.89[AFR][1000 genomes]
rs73018621	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018622	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018628	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73018640	1.00[EUR][1000 genomes]
rs73018641	1.00[EUR][1000 genomes]
rs73019085	1.00[EUR][1000 genomes]
rs73019091	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73019099	0.81[AFR][1000 genomes]
rs7615523	1.00[EUR][1000 genomes]
rs7616375	0.89[YRI][hapmap];1.00[EUR][1000 genomes]
rs7638986	0.83[YRI][hapmap];0.86[AFR][1000 genomes]
rs7650189	1.00[EUR][1000 genomes]
rs7650499	1.00[EUR][1000 genomes]
rs7650959	0.82[YRI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs906766	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs9917673	1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2757897	chr3:150791625-150957485	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2759188	chr3:150791625-150957485	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv877648	chr3:150792444-150895145	Enhancers Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150872800-150910800	Weak transcription	Brain Germinal Matrix	brain
2	chr3:150873200-150910200	Weak transcription	Brain Angular Gyrus	brain
3	chr3:150873800-150890000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr3:150873800-150890000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr3:150873800-150913800	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:150874200-150896000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr3:150874800-150900200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
8	chr3:150878000-150946000	Weak transcription	Placenta	Placenta
9	chr3:150878400-150890800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr3:150880400-150900200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr3:150880800-150900400	Weak transcription	Brain Cingulate Gyrus	brain
12	chr3:150883800-150896000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr3:150884200-150906600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:150884400-150893400	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr3:150886000-150890800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr3:150886200-150890400	Enhancers	Primary T cells fromperipheralblood	blood
17	chr3:150886200-150890400	Enhancers	Primary T helper cells fromperipheralblood	blood
18	chr3:150886200-150890400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr3:150886200-150890800	Enhancers	Primary hematopoietic stem cells	blood
20	chr3:150886200-150890800	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr3:150886200-150892400	Enhancers	Primary T cells from cord blood	blood
22	chr3:150886200-150893000	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr3:150886600-150890200	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr3:150886600-150890400	Enhancers	Fetal Thymus	thymus
25	chr3:150886800-150892600	Weak transcription	Liver	Liver
26	chr3:150887600-150890000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr3:150887600-150890000	Enhancers	Thymus	Thymus
28	chr3:150887600-150891000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr3:150888000-150890000	Enhancers	Primary neutrophils fromperipheralblood	blood
30	chr3:150888000-150890000	Enhancers	Primary B cells from cord blood	blood
31	chr3:150888000-150890200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:150888200-150890000	Enhancers	HepG2	liver
33	chr3:150888400-150890000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
34	chr3:150888400-150893800	Weak transcription	Small Intestine	intestine
35	chr3:150888600-150890000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr3:150888600-150896000	Weak transcription	Stomach Mucosa	stomach
37	chr3:150888800-150890200	Weak transcription	Adipose Nuclei	Adipose
38	chr3:150888800-150891000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:150888800-150896000	Weak transcription	Duodenum Mucosa	Duodenum
40	chr3:150889000-150904000	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr3:150889200-150890400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr3:150889200-150890800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:150889200-150891000	Enhancers	Primary T helper naive cells from peripheral blood	blood
44	chr3:150889200-150908200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:150889200-150914800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr3:150889400-150890000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:150889400-150891200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr3:150889400-150896200	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:150889400-150903600	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr3:150889600-150890800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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