Variant report

Variant	rs16829179
Chromosome Location	chr3:118668260-118668261
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	chr3:118654131..118656982-chr3:118667151..118670304,3	K562	blood:
2	chr3:118655482..118657417-chr3:118667049..118669730,2	K562	blood:

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1158699	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12485923	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12492855	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12495725	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12496820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1435655	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs2160054	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28484956	0.82[AFR][1000 genomes]
rs28565574	0.85[AFR][1000 genomes]
rs28573387	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28592657	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28655404	0.82[AFR][1000 genomes]
rs3821882	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4611809	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56728928	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58284747	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6772441	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773865	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs6779428	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6795721	0.87[ASW][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.86[AFR][1000 genomes]
rs6796798	0.84[MKK][hapmap]
rs6807110	1.00[CEU][hapmap];0.94[MEX][hapmap]
rs6807838	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72966895	0.83[AFR][1000 genomes]
rs72968605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968610	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72968613	0.85[AFR][1000 genomes]
rs72968638	0.86[AFR][1000 genomes]
rs7633584	1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9811829	0.86[AFR][1000 genomes]
rs9817943	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9821022	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9821458	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9826100	0.82[YRI][hapmap]
rs9828087	0.85[AFR][1000 genomes]
rs9828870	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9833229	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836642	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9849421	0.85[AFR][1000 genomes]
rs9855713	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860140	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867214	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9873807	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9874208	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9874337	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3487859	chr3:118570588-119419623	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	61 gene(s)	inside rSNPs	diseases
2	esv3487860	chr3:118570588-119419623	Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv1010475	chr3:118657382-118789714	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16829179	NCAPD2	trans	brain	seeQTL

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:118658000-118668400	Weak transcription	A549	lung
2	chr3:118662000-118679800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr3:118662000-118679800	Weak transcription	Ovary	ovary
4	chr3:118662800-118672000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr3:118662800-118672400	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:118664400-118676400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr3:118665600-118668800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:118665600-118669000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:118666200-118677800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr3:118666400-118669800	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr3:118666600-118668400	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr3:118666600-118669200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr3:118666600-118669800	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr3:118666600-118670200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr3:118666800-118669200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr3:118666800-118669400	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr3:118666800-118669400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr3:118667000-118668800	Enhancers	Primary T cells fromperipheralblood	blood
19	chr3:118667000-118668800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:118667200-118668800	Enhancers	Brain Hippocampus Middle	brain
21	chr3:118667200-118668800	Enhancers	Placenta	Placenta
22	chr3:118667400-118668400	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:118667800-118668800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
24	chr3:118668000-118668400	Flanking Active TSS	Primary T cells from cord blood	blood
25	chr3:118668000-118668600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr3:118668000-118669800	Enhancers	Brain Substantia Nigra	brain
27	chr3:118668000-118670000	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:118668200-118668600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr3:118668200-118668600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr3:118668200-118668600	Enhancers	iPS-15b Cell Line	embryonic stem cell
31	chr3:118668200-118668600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr3:118668200-118668800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr3:118668200-118668800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:118668200-118669000	Enhancers	Fetal Heart	heart
35	chr3:118668200-118669200	Enhancers	Brain Angular Gyrus	brain
36	chr3:118668200-118670000	Enhancers	Brain Anterior Caudate	brain

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