Variant report

Variant	rs4666299
Chromosome Location	chr2:20467929-20467930
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20467246..20470350-chr2:20472212..20474237,3	K562	blood:
2	chr2:20463108..20465491-chr2:20466450..20468569,2	K562	blood:
3	chr2:20466339..20468775-chr2:20471320..20473308,2	MCF-7	breast:

Extended variants
information (count: 36 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10175853	0.80[JPT][hapmap]
rs10190763	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10192042	0.80[JPT][hapmap]
rs1043400	0.80[JPT][hapmap]
rs11096655	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[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];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11679966	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11683916	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11686919	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11888357	0.80[JPT][hapmap]
rs11895228	0.82[JPT][hapmap]
rs11896241	0.80[JPT][hapmap]
rs2110409	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2160072	0.88[CEU][hapmap];0.83[CHB][hapmap]
rs2348704	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs343163	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs343164	1.00[CEU][hapmap];0.83[CHB][hapmap];0.96[TSI][hapmap];0.85[EUR][1000 genomes]
rs343165	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3771228	0.95[CEU][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3796066	0.80[JPT][hapmap]
rs3821218	0.80[JPT][hapmap]
rs4666304	0.86[EUR][1000 genomes]
rs4666305	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4666382	1.00[CEU][hapmap];0.89[CHB][hapmap];0.98[GIH][hapmap];0.84[JPT][hapmap];0.96[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4666383	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6531232	1.00[CEU][hapmap];0.89[CHB][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6713329	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6730690	0.87[ASW][hapmap];0.92[LWK][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs6748274	0.80[JPT][hapmap]
rs6750331	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6756819	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7355288	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7563245	0.80[JPT][hapmap]
rs7596797	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9306890	0.80[JPT][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	nsv524207	chr2:20448561-20503436	Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv999153	chr2:20467929-20521954	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4666299	HS1BP3	cis	parietal	SCAN
rs4666299	WDR35	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20442000-20491000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:20442800-20474800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:20444400-20489000	Weak transcription	Stomach Mucosa	stomach
4	chr2:20445400-20473800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr2:20446400-20473600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:20447000-20468600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr2:20447000-20470200	Strong transcription	Dnd41	blood
8	chr2:20452000-20481600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:20454200-20471600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:20454200-20480800	Weak transcription	Aorta	Aorta
11	chr2:20454200-20480800	Weak transcription	Psoas Muscle	Psoas
12	chr2:20454200-20482800	Weak transcription	Pancreas	Pancrea
13	chr2:20454200-20488800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:20454200-20490800	Weak transcription	Right Ventricle	heart
15	chr2:20454200-20491000	Weak transcription	Gastric	stomach
16	chr2:20454200-20491000	Weak transcription	Spleen	Spleen
17	chr2:20454200-20499600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:20454400-20481600	Weak transcription	Brain Angular Gyrus	brain
19	chr2:20455400-20481600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr2:20455400-20482600	Weak transcription	Ovary	ovary
21	chr2:20455800-20481600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:20455800-20485000	Weak transcription	Colonic Mucosa	Colon
23	chr2:20456400-20482600	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr2:20456400-20488800	Weak transcription	Small Intestine	intestine
25	chr2:20456600-20477800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr2:20458000-20491000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr2:20459800-20478000	Weak transcription	Fetal Heart	heart
28	chr2:20459800-20480800	Weak transcription	Brain Inferior Temporal Lobe	brain
29	chr2:20459800-20481600	Weak transcription	Brain Anterior Caudate	brain
30	chr2:20459800-20481600	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr2:20460000-20476600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr2:20460000-20480600	Weak transcription	Brain Hippocampus Middle	brain
33	chr2:20460200-20481000	Weak transcription	HMEC	breast
34	chr2:20460200-20528600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:20460800-20471800	Weak transcription	HSMMtube	muscle
36	chr2:20460800-20480600	Weak transcription	Rectal Smooth Muscle	rectum
37	chr2:20460800-20481600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr2:20460800-20485800	Weak transcription	Fetal Brain Male	brain
39	chr2:20461000-20480000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr2:20461000-20481800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr2:20461800-20469600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr2:20461800-20477800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
43	chr2:20462200-20480800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr2:20462200-20482400	Weak transcription	Brain Germinal Matrix	brain
45	chr2:20462400-20480800	Weak transcription	Left Ventricle	heart
46	chr2:20462600-20477200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:20462600-20480800	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr2:20462600-20482200	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr2:20463000-20468600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr2:20463000-20476600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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