Variant report

Variant	rs949882
Chromosome Location	chr6:109586062-109586063
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:109586028..109588133-chr6:109739017..109740783,2	K562	blood:
2	chr6:109580166..109583539-chr6:109585250..109587755,3	MCF-7	breast:
3	chr6:109572844..109579013-chr6:109586013..109590515,6	MCF-7	breast:

Extended variants
information (count: 114 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1040285	0.89[ASW][hapmap]
rs1111863	0.82[YRI][hapmap]
rs1111865	0.82[LWK][hapmap]
rs1111866	0.82[LWK][hapmap]
rs1113665	0.89[ASW][hapmap]
rs11153165	0.83[CEU][hapmap]
rs11153166	0.83[CEU][hapmap]
rs11153167	0.83[CEU][hapmap]
rs1260595	0.91[JPT][hapmap]
rs1260596	0.90[JPT][hapmap]
rs13195816	0.93[ASN][1000 genomes]
rs13210424	0.93[ASN][1000 genomes]
rs13210693	0.91[ASN][1000 genomes]
rs1341272	0.91[JPT][hapmap]
rs1521905	0.93[ASN][1000 genomes]
rs1608041	0.93[ASN][1000 genomes]
rs1608042	0.93[ASN][1000 genomes]
rs1608044	0.93[ASN][1000 genomes]
rs1741930	0.91[JPT][hapmap]
rs1761608	0.86[JPT][hapmap]
rs1829694	0.93[ASN][1000 genomes]
rs1915834	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1915835	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs2222392	0.90[ASN][1000 genomes]
rs2884012	0.93[ASN][1000 genomes]
rs2884013	0.91[ASN][1000 genomes]
rs34981677	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs351736	0.84[CEU][hapmap]
rs351737	0.84[CEU][hapmap]
rs35492211	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs368467	0.90[JPT][hapmap]
rs396000	0.91[JPT][hapmap]
rs419106	0.91[JPT][hapmap]
rs4383852	0.93[ASN][1000 genomes]
rs4406271	0.93[ASN][1000 genomes]
rs4427037	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4601178	0.82[LWK][hapmap]
rs566164	0.83[CEU][hapmap]
rs6568558	0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6568559	0.93[ASN][1000 genomes]
rs6568560	0.92[ASN][1000 genomes]
rs6568561	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs6568564	0.93[ASN][1000 genomes]
rs6568566	0.93[ASN][1000 genomes]
rs6568567	0.92[ASN][1000 genomes]
rs6568568	0.93[ASN][1000 genomes]
rs6899616	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6903107	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6910119	0.91[ASN][1000 genomes]
rs6910696	0.95[ASN][1000 genomes]
rs6925339	0.84[CEU][hapmap]
rs6925716	0.93[ASN][1000 genomes]
rs6928622	0.93[ASN][1000 genomes]
rs6929438	0.91[ASN][1000 genomes]
rs6930526	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6930693	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6930698	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6930844	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6933326	0.91[ASN][1000 genomes]
rs7748641	0.96[ASN][1000 genomes]
rs7753697	0.92[ASN][1000 genomes]
rs7753705	0.92[ASN][1000 genomes]
rs7755970	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7765166	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7772602	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs7773213	0.91[ASN][1000 genomes]
rs7773490	0.83[CEU][hapmap]
rs7773775	0.91[ASN][1000 genomes]
rs7773815	0.89[ASN][1000 genomes]
rs7774377	0.91[ASN][1000 genomes]
rs7774390	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7775206	0.93[ASN][1000 genomes]
rs932223	0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9372205	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9372208	0.93[ASN][1000 genomes]
rs9372209	0.91[ASN][1000 genomes]
rs9372210	0.91[ASN][1000 genomes]
rs9374067	0.89[ASW][hapmap]
rs9374069	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374070	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];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9374071	1.00[CEU][hapmap];1.00[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];0.98[ASN][1000 genomes]
rs9374072	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];0.99[ASN][1000 genomes]
rs9374077	0.91[ASN][1000 genomes]
rs9384703	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9384704	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9384705	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9384706	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9386781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9386783	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9386784	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9386787	0.90[ASN][1000 genomes]
rs9386788	0.91[ASN][1000 genomes]
rs9386789	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9386790	0.82[LWK][hapmap]
rs9398191	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9398192	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];0.99[ASN][1000 genomes]
rs9398193	0.92[ASN][1000 genomes]
rs9398196	0.91[ASN][1000 genomes]
rs9400262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9400266	0.93[ASN][1000 genomes]
rs9400267	0.91[ASN][1000 genomes]
rs9400268	0.91[ASN][1000 genomes]
rs9400269	0.82[LWK][hapmap]
rs9400271	0.80[CEU][hapmap]
rs9480921	0.82[LWK][hapmap]
rs9480922	0.81[YRI][hapmap]
rs9480923	0.85[YRI][hapmap]
rs9487020	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9487033	0.82[YRI][hapmap]
rs9487034	0.82[LWK][hapmap]
rs949881	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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784763	0.81[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][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	esv999906	chr6:109584769-109588060	Weak transcription Enhancers Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs949882	ATG5	cis	cerebellum	SCAN
rs949882	CD164	cis	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109564000-109590400	Weak transcription	Psoas Muscle	Psoas
2	chr6:109572800-109590400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr6:109572800-109595200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:109573200-109589800	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr6:109573600-109590200	Weak transcription	Gastric	stomach
6	chr6:109575800-109589200	Weak transcription	Pancreas	Pancrea
7	chr6:109581800-109588800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:109583000-109587600	Strong transcription	HepG2	liver
9	chr6:109583400-109587200	Weak transcription	Adipose Nuclei	Adipose
10	chr6:109583400-109587600	Strong transcription	Placenta	Placenta
11	chr6:109583400-109590400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:109583600-109590200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:109583600-109590400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr6:109583600-109591400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:109583800-109590400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr6:109585000-109586600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:109585200-109586800	Enhancers	K562	blood
18	chr6:109585600-109586600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr6:109585800-109587200	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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