Variant report

Variant	rs1869857
Chromosome Location	chr3:157123357-157123358
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10936086	0.81[EUR][1000 genomes]
rs10936087	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs10936088	0.81[TSI][hapmap]
rs10936090	0.80[JPT][hapmap]
rs12486427	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs12492874	0.83[EUR][1000 genomes]
rs12492929	0.83[EUR][1000 genomes]
rs12636038	0.83[EUR][1000 genomes]
rs12638732	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs13087207	0.83[EUR][1000 genomes]
rs1392798	0.84[CEU][hapmap]
rs1456097	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs1456105	0.83[EUR][1000 genomes]
rs1456106	0.83[EUR][1000 genomes]
rs1456108	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1456110	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1500916	0.84[CEU][hapmap]
rs1545596	0.84[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1563420	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1585080	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs1824058	0.87[CEU][hapmap]
rs1840668	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs1840673	0.83[CEU][hapmap];0.80[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1840680	0.80[JPT][hapmap]
rs1869859	0.84[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1965246	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2047649	0.84[CEU][hapmap]
rs2085315	0.83[EUR][1000 genomes]
rs2120243	0.80[JPT][hapmap]
rs2124497	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2168430	0.84[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2168431	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2305619	0.85[JPT][hapmap]
rs2305620	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2305622	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2316709	0.80[JPT][hapmap]
rs28638274	0.94[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.96[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap]
rs35004310	0.83[EUR][1000 genomes]
rs3816528	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4435581	0.83[EUR][1000 genomes]
rs4482625	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4640512	0.84[CEU][hapmap];0.83[EUR][1000 genomes]
rs4640513	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4679793	0.84[CEU][hapmap];0.83[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4680360	0.81[TSI][hapmap];0.80[EUR][1000 genomes]
rs56249701	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6441127	0.82[EUR][1000 genomes]
rs6441128	0.83[CEU][hapmap];0.83[EUR][1000 genomes]
rs6441129	0.84[CEU][hapmap];0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs6801110	0.84[CEU][hapmap]
rs6803628	0.81[EUR][1000 genomes]
rs722484	0.83[EUR][1000 genomes]
rs7615621	0.80[JPT][hapmap]
rs7617727	0.84[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs7618502	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7618737	0.82[EUR][1000 genomes]
rs7623173	0.82[CEU][hapmap];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7629293	0.83[EUR][1000 genomes]
rs7639254	0.80[CEU][hapmap];0.81[TSI][hapmap]
rs9681270	0.80[JPT][hapmap]
rs9857875	0.83[CEU][hapmap]
rs9871290	0.83[CEU][hapmap];0.81[TSI][hapmap];0.82[EUR][1000 genomes]
rs9878474	0.84[CEU][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes]
rs988587	0.84[CEU][hapmap]
rs988588	0.84[CEU][hapmap]
rs9990136	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2757900	chr3:157090166-157254684	Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	esv2759193	chr3:157090166-157254684	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1869857	BRD7	cis	cerebellum	SCAN
rs1869857	SSR3	cis	cerebellum	SCAN
rs1869857	PTX3	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:157091800-157142600	Weak transcription	Pancreas	Pancrea
2	chr3:157107400-157128000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr3:157113400-157129800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:157116000-157128600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:157119000-157142800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr3:157120000-157142600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr3:157120200-157135800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:157122600-157123800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:157122600-157124600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr3:157122800-157124200	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:157122800-157124400	Enhancers	Osteobl	bone
12	chr3:157123000-157123800	Enhancers	NH-A	brain
13	chr3:157123000-157124000	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:157123000-157124200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr3:157123000-157124400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:157123000-157124600	Enhancers	Muscle Satellite Cultured Cells	--
17	chr3:157123000-157125800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr3:157123000-157126600	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr3:157123000-157135000	Weak transcription	Spleen	Spleen
20	chr3:157123200-157123600	Enhancers	NHDF-Ad	bronchial
21	chr3:157123200-157124200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr3:157123200-157124400	Enhancers	HSMM	muscle
23	chr3:157123200-157124600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:157123200-157124800	Genic enhancers	HUVEC	blood vessel

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