Variant report

Variant	rs16870407
Chromosome Location	chr5:40853048-40853049
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40832678..40834651-chr5:40851287..40853714,2	K562	blood:
2	chr5:40839582..40842415-chr5:40852942..40856062,3	K562	blood:
3	chr5:40798425..40801370-chr5:40851510..40853477,2	K562	blood:
4	chr5:40835369..40837107-chr5:40851316..40853439,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000132357	Chromatin interaction
ENSG00000145592	Chromatin interaction
ENSG00000132356	Chromatin interaction
ENSG00000212296	Chromatin interaction

Extended variants
information (count: 99 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs10035235	0.86[ASW][hapmap]
rs10035592	0.81[ASN][1000 genomes]
rs10035621	0.89[ASN][1000 genomes]
rs10041257	0.89[ASN][1000 genomes]
rs10041319	0.98[ASN][1000 genomes]
rs10046046	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10058274	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[ASN][1000 genomes]
rs10060965	0.81[ASN][1000 genomes]
rs10063892	0.89[ASN][1000 genomes]
rs10066341	0.82[EUR][1000 genomes]
rs10072099	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10072214	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10472340	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10473227	0.81[ASN][1000 genomes]
rs10473228	0.81[ASN][1000 genomes]
rs10512750	0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs10941526	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.97[ASN][1000 genomes]
rs10941527	0.82[ASN][1000 genomes]
rs1120308	0.81[ASN][1000 genomes]
rs11739731	0.81[ASN][1000 genomes]
rs11741315	0.81[ASN][1000 genomes]
rs11746650	0.95[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs12523329	0.86[ASW][hapmap]
rs12652909	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12657195	0.81[ASN][1000 genomes]
rs12658133	0.94[JPT][hapmap];0.81[ASN][1000 genomes]
rs13353861	0.96[ASN][1000 genomes]
rs13353862	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13353865	0.98[ASN][1000 genomes]
rs13354307	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13355045	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1393155	0.82[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap]
rs1615402	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs1645519	0.81[CHD][hapmap];0.86[GIH][hapmap]
rs16870425	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.82[MEX][hapmap];0.81[MKK][hapmap];0.98[ASN][1000 genomes]
rs16870434	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16870491	0.81[ASN][1000 genomes]
rs17175825	0.82[EUR][1000 genomes]
rs188932	0.81[CHB][hapmap];0.83[ASN][1000 genomes]
rs2081153	1.00[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs225749	0.86[ASN][1000 genomes]
rs2291782	0.86[ASW][hapmap]
rs2329430	0.81[ASN][1000 genomes]
rs2329431	0.85[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs2455307	0.92[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs2455308	0.92[CHD][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs28718806	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2876848	0.81[ASN][1000 genomes]
rs28770573	0.81[ASN][1000 genomes]
rs28834109	0.80[ASN][1000 genomes]
rs28860325	0.81[ASN][1000 genomes]
rs28870511	0.81[ASN][1000 genomes]
rs323555	0.86[ASN][1000 genomes]
rs323557	0.86[ASN][1000 genomes]
rs323558	0.85[ASN][1000 genomes]
rs323559	0.86[ASN][1000 genomes]
rs323563	0.85[ASN][1000 genomes]
rs323564	0.83[ASN][1000 genomes]
rs323566	0.85[CHB][hapmap];0.80[CHD][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs34888872	0.81[ASN][1000 genomes]
rs369331	0.85[CHB][hapmap];0.80[JPT][hapmap];0.85[ASN][1000 genomes]
rs3792640	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3792641	0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3805490	0.86[ASW][hapmap]
rs3805492	0.86[ASW][hapmap]
rs4277954	0.81[ASN][1000 genomes]
rs439322	0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[ASN][1000 genomes]
rs4461680	0.81[ASN][1000 genomes]
rs446920	0.86[ASN][1000 genomes]
rs4559041	0.81[ASN][1000 genomes]
rs619491	0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap]
rs62357601	0.94[ASN][1000 genomes]
rs62357603	0.94[ASN][1000 genomes]
rs62357605	0.96[ASN][1000 genomes]
rs62357612	0.98[ASN][1000 genomes]
rs62357636	0.89[ASN][1000 genomes]
rs62357641	0.89[ASN][1000 genomes]
rs62358575	0.81[ASN][1000 genomes]
rs72748000	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72749504	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72749508	0.98[ASN][1000 genomes]
rs72749510	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72749514	0.89[ASN][1000 genomes]
rs72749526	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7701643	0.81[ASN][1000 genomes]
rs7701871	0.81[ASN][1000 genomes]
rs7704691	0.81[ASN][1000 genomes]
rs7706776	0.81[ASN][1000 genomes]
rs7717457	0.84[CHD][hapmap];0.89[GIH][hapmap];0.82[MEX][hapmap]
rs7717794	0.81[ASN][1000 genomes]
rs7724262	0.81[ASN][1000 genomes]
rs837387	0.84[ASN][1000 genomes]
rs9292793	0.81[ASN][1000 genomes]
rs9292794	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9292795	0.81[ASN][1000 genomes]
rs972007	0.81[ASN][1000 genomes]
rs972008	0.81[ASN][1000 genomes]
rs9885543	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16870407	MGC42105	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40842200-40853800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr5:40842400-40853400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:40842400-40853800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:40842400-40854200	Weak transcription	Fetal Stomach	stomach
5	chr5:40842400-40854600	Weak transcription	Brain Hippocampus Middle	brain
6	chr5:40842800-40853200	Weak transcription	Fetal Intestine Small	intestine
7	chr5:40842800-40854000	Weak transcription	Aorta	Aorta
8	chr5:40842800-40856000	Weak transcription	Right Ventricle	heart
9	chr5:40843600-40854000	Weak transcription	Colon Smooth Muscle	Colon
10	chr5:40843600-40857800	Weak transcription	Osteobl	bone
11	chr5:40849800-40854800	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr5:40849800-40856000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr5:40849800-40857400	Weak transcription	Primary B cells from cord blood	blood
14	chr5:40850200-40854000	Weak transcription	Primary B cells from peripheral blood	blood
15	chr5:40851200-40855400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr5:40851400-40853400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:40851400-40854400	Weak transcription	HSMMtube	muscle
18	chr5:40851400-40855000	Strong transcription	Primary monocytes fromperipheralblood	blood
19	chr5:40851800-40854400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:40851800-40854800	Strong transcription	Lung	lung
21	chr5:40851800-40856200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:40852000-40853800	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr5:40852000-40854000	Weak transcription	Stomach Smooth Muscle	stomach
24	chr5:40852000-40854400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr5:40852000-40854600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:40852000-40854600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr5:40852000-40854600	Strong transcription	Adipose Nuclei	Adipose
28	chr5:40852000-40854600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr5:40852000-40854600	Strong transcription	Spleen	Spleen
30	chr5:40852000-40856000	Weak transcription	Fetal Lung	lung
31	chr5:40852000-40856400	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr5:40852200-40854000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr5:40852200-40854800	Strong transcription	Duodenum Mucosa	Duodenum
34	chr5:40852400-40853400	Strong transcription	Hela-S3	cervix
35	chr5:40852400-40853400	Strong transcription	HUVEC	blood vessel
36	chr5:40852400-40854000	Strong transcription	Esophagus	oesophagus
37	chr5:40852400-40854200	Strong transcription	Liver	Liver
38	chr5:40852400-40854400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
39	chr5:40852400-40854600	Strong transcription	Gastric	stomach
40	chr5:40852600-40853400	Strong transcription	Small Intestine	intestine
41	chr5:40852600-40854000	Strong transcription	Primary T cells from cord blood	blood
42	chr5:40852600-40855200	Strong transcription	Placenta	Placenta
43	chr5:40852800-40853600	Weak transcription	Ovary	ovary
44	chr5:40852800-40865200	Weak transcription	Pancreas	Pancrea
45	chr5:40853000-40854600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr5:40853000-40856200	Weak transcription	Left Ventricle	heart

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