Variant report

Variant	rs990569
Chromosome Location	chr2:72975980-72975981
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	chr2:72975058..72976959-chr2:72978477..72981008,2	MCF-7	breast:
2	chr2:72971179..72973717-chr2:72974748..72977332,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10183056	1.00[ASN][1000 genomes]
rs10206555	1.00[ASN][1000 genomes]
rs10211019	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1032982	1.00[CHB][hapmap]
rs10460572	1.00[ASN][1000 genomes]
rs10496186	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10865391	1.00[ASN][1000 genomes]
rs10865392	0.92[CEU][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs11126370	1.00[ASN][1000 genomes]
rs11126371	1.00[ASN][1000 genomes]
rs11126372	1.00[ASN][1000 genomes]
rs11126373	1.00[ASN][1000 genomes]
rs11126374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs11126376	1.00[CHB][hapmap]
rs11126385	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150500	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap]
rs1161265	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap]
rs1161267	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs11676555	1.00[CHB][hapmap]
rs11677707	1.00[CHB][hapmap]
rs11679683	1.00[CHB][hapmap]
rs11684985	1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11685114	1.00[CHB][hapmap]
rs11686713	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs11894160	0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs12471312	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs12476130	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs12618390	1.00[ASN][1000 genomes]
rs12713772	1.00[ASN][1000 genomes]
rs12713773	1.00[ASN][1000 genomes]
rs12713774	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12713775	0.91[CEU][hapmap];1.00[CHD][hapmap];0.85[MEX][hapmap];0.94[TSI][hapmap];0.81[EUR][1000 genomes]
rs12989141	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12996319	1.00[CHB][hapmap]
rs12996406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12998681	1.00[ASN][1000 genomes]
rs13006497	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs13008041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs13008258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs13011477	1.00[CHB][hapmap]
rs13016873	1.00[ASN][1000 genomes]
rs1396106	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1400580	1.00[ASN][1000 genomes]
rs1446887	1.00[CHB][hapmap]
rs1446888	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[GIH][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs1446889	1.00[ASN][1000 genomes]
rs1446890	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs1446891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs1446892	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs1446893	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[ASN][1000 genomes]
rs1446895	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1446896	1.00[CHB][hapmap]
rs1508061	1.00[CHB][hapmap]
rs1567230	0.91[CEU][hapmap];1.00[CHD][hapmap];0.87[TSI][hapmap]
rs1596930	1.00[CHB][hapmap]
rs1596931	1.00[CHB][hapmap]
rs1711838	1.00[ASN][1000 genomes]
rs17503444	1.00[CHB][hapmap]
rs1911690	1.00[CHB][hapmap]
rs1992799	1.00[ASN][1000 genomes]
rs1995734	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2138683	1.00[ASN][1000 genomes]
rs2420565	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2420880	0.91[CEU][hapmap]
rs2421095	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[TSI][hapmap]
rs4144318	1.00[ASN][1000 genomes]
rs4321391	0.91[CEU][hapmap]
rs4364045	1.00[CHB][hapmap]
rs4407272	1.00[ASN][1000 genomes]
rs4852291	1.00[ASN][1000 genomes]
rs4852292	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs4852293	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852294	1.00[ASN][1000 genomes]
rs4852298	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4852872	1.00[ASN][1000 genomes]
rs4852875	1.00[ASN][1000 genomes]
rs4852876	1.00[ASN][1000 genomes]
rs4852877	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4852878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.93[TSI][hapmap];1.00[ASN][1000 genomes]
rs4852880	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs4852883	1.00[CHB][hapmap];1.00[CHD][hapmap]
rs4852886	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap]
rs4852888	1.00[CHB][hapmap]
rs4852889	1.00[CHB][hapmap]
rs4852890	1.00[CHB][hapmap]
rs4852891	1.00[CHB][hapmap]
rs4852893	0.91[CEU][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583673	1.00[ASN][1000 genomes]
rs585938	1.00[ASN][1000 genomes]
rs632670	1.00[ASN][1000 genomes]
rs645489	1.00[ASN][1000 genomes]
rs646357	1.00[ASN][1000 genomes]
rs650352	1.00[ASN][1000 genomes]
rs654157	1.00[ASN][1000 genomes]
rs6546776	1.00[ASN][1000 genomes]
rs6546777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6546778	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6546779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546781	1.00[CHB][hapmap]
rs6546782	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6546783	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6707435	1.00[ASN][1000 genomes]
rs6714580	1.00[ASN][1000 genomes]
rs671721	1.00[ASN][1000 genomes]
rs6724529	1.00[CHB][hapmap]
rs6730083	0.91[CEU][hapmap];1.00[CHB][hapmap]
rs6736305	1.00[ASN][1000 genomes]
rs6739002	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6742088	1.00[ASN][1000 genomes]
rs6742312	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6747378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6750766	1.00[ASN][1000 genomes]
rs683328	1.00[ASN][1000 genomes]
rs684673	1.00[ASN][1000 genomes]
rs7420391	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7560529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7560599	1.00[ASN][1000 genomes]
rs7565198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7571064	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[TSI][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7577238	1.00[CHB][hapmap]
rs7580268	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7586787	0.81[EUR][1000 genomes]
rs7588400	1.00[CHB][hapmap]
rs7588602	0.91[CEU][hapmap];1.00[CHB][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7591025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7591303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7592155	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7598238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7601020	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.94[TSI][hapmap];1.00[ASN][1000 genomes]
rs7601318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs7603797	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs983928	1.00[ASN][1000 genomes]

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	nsv874265	chr2:72789764-72982609	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv834259	chr2:72941118-73114106	Enhancers Active TSS Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs990569	CYP26B1	cis	Whole Blood	GTEx
rs990569	CYP26B1	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:72905800-72984400	Weak transcription	Aorta	Aorta
2	chr2:72922400-72976200	Weak transcription	Psoas Muscle	Psoas
3	chr2:72923000-73008600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr2:72937800-72978400	Weak transcription	Brain Germinal Matrix	brain
5	chr2:72938200-72987800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:72943600-72978800	Weak transcription	Primary T cells from cord blood	blood
7	chr2:72945600-72977800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:72946800-72980200	Weak transcription	Left Ventricle	heart
9	chr2:72950000-72982400	Weak transcription	Colon Smooth Muscle	Colon
10	chr2:72961200-72976400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:72968600-72980000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:72971200-72976000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr2:72971200-72977200	Weak transcription	Stomach Mucosa	stomach
14	chr2:72971800-72982800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr2:72972200-72980400	Weak transcription	Right Ventricle	heart
16	chr2:72972800-72982600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr2:72973000-72976000	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr2:72973000-72982200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr2:72973000-72982600	Weak transcription	Hela-S3	cervix
20	chr2:72973200-72977400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr2:72974200-72976000	Enhancers	Brain Hippocampus Middle	brain
22	chr2:72974600-72976000	Enhancers	Fetal Lung	lung
23	chr2:72974600-72981000	Enhancers	Fetal Heart	heart
24	chr2:72974800-72982200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:72975000-72976000	Enhancers	Ovary	ovary
26	chr2:72975200-72982800	Weak transcription	Brain Substantia Nigra	brain
27	chr2:72975600-72976000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr2:72975600-72976200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr2:72975600-72976400	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:72975600-72978200	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:72975800-72976200	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr2:72975800-72977200	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr2:72975800-72977800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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