Variant report

Variant	rs2066202
Chromosome Location	chr6:107003810-107003811
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	chr6:107002175..107004858-chr6:107006696..107008567,2	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1037955	0.81[CEU][hapmap];0.87[GIH][hapmap]
rs11759221	0.98[ASN][1000 genomes]
rs11968064	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.81[MEX][hapmap];0.98[ASN][1000 genomes]
rs12523774	0.91[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12526141	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs13319	0.81[CEU][hapmap]
rs1419054	0.94[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.82[TSI][hapmap]
rs1676016	0.91[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap];0.81[EUR][1000 genomes]
rs17052215	0.94[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs17067368	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs1770728	0.91[CEU][hapmap]
rs1770731	0.90[CEU][hapmap]
rs1770732	0.91[CEU][hapmap]
rs2054366	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[GIH][hapmap];0.98[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes]
rs2126395	0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2219667	0.84[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2297971	1.00[ASW][hapmap];0.91[CEU][hapmap];0.87[GIH][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs2353043	0.84[AMR][1000 genomes]
rs2615206	0.81[CEU][hapmap]
rs2615207	0.81[CEU][hapmap];0.87[GIH][hapmap];0.97[TSI][hapmap]
rs3747790	0.91[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4523123	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs4945759	0.81[CEU][hapmap];0.82[MKK][hapmap];0.91[TSI][hapmap]
rs4946763	0.94[ASN][1000 genomes]
rs4946764	0.81[CEU][hapmap];0.87[GIH][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap]
rs57424436	0.98[ASN][1000 genomes]
rs58972320	0.98[ASN][1000 genomes]
rs6903754	0.81[CEU][hapmap]
rs6907164	0.81[CEU][hapmap]
rs6926307	0.81[CEU][hapmap]
rs6926670	0.81[CEU][hapmap]
rs6926833	0.81[CEU][hapmap]
rs7738230	0.94[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs7741101	0.81[CEU][hapmap];0.94[TSI][hapmap]
rs7755346	0.99[AFR][1000 genomes]
rs7770930	0.81[CEU][hapmap]
rs7776287	0.81[CEU][hapmap]
rs7776294	0.81[CEU][hapmap]
rs8013	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9320182	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9320183	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9384622	0.93[ASN][1000 genomes]
rs9386567	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9398095	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9480684	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9480685	0.81[CEU][hapmap]
rs9480686	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9480687	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9480689	0.81[CEU][hapmap];0.83[GIH][hapmap];0.94[TSI][hapmap]
rs9486398	0.81[CEU][hapmap]
rs9486399	0.81[CEU][hapmap]
rs9486400	0.87[GIH][hapmap]
rs9486404	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9486406	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9486410	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9486411	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs9486414	0.91[CEU][hapmap];0.96[GIH][hapmap];0.94[TSI][hapmap]
rs9486415	0.81[CEU][hapmap];0.87[GIH][hapmap];0.94[TSI][hapmap]
rs965347	0.81[CEU][hapmap]
rs9689006	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932155	chr6:106281728-107030467	Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv532047	chr6:106591482-107143252	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv870375	chr6:106696090-107047892	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2066202	QRSL1	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:106964800-107029800	Weak transcription	Small Intestine	intestine
2	chr6:106970600-107022400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:106985800-107019200	Weak transcription	Aorta	Aorta
4	chr6:106994000-107017800	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:106994200-107009000	Weak transcription	Left Ventricle	heart
6	chr6:106994200-107019400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr6:106994200-107019600	Strong transcription	Primary T cells fromperipheralblood	blood
8	chr6:106994800-107004200	Strong transcription	Primary T cells from cord blood	blood
9	chr6:106994800-107004600	Strong transcription	Rectal Mucosa Donor 29	rectum
10	chr6:106994800-107004600	Weak transcription	Hela-S3	cervix
11	chr6:106995000-107019400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:106995200-107016200	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:106995200-107018800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr6:106995800-107004400	Strong transcription	Rectal Mucosa Donor 31	rectum
15	chr6:106996200-107017200	Weak transcription	HSMM	muscle
16	chr6:106996200-107018400	Weak transcription	Fetal Stomach	stomach
17	chr6:106996200-107022400	Weak transcription	Ovary	ovary
18	chr6:106996200-107023000	Weak transcription	Stomach Mucosa	stomach
19	chr6:106996400-107005600	Weak transcription	Osteobl	bone
20	chr6:106996400-107009000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr6:106996400-107012200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr6:106996400-107027000	Strong transcription	Primary B cells from peripheral blood	blood
23	chr6:106996400-107030800	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:106996400-107074000	Weak transcription	Fetal Kidney	kidney
25	chr6:106996600-107009200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr6:106996600-107009600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr6:106996600-107012000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr6:106996600-107018400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr6:106996600-107022400	Weak transcription	HUVEC	blood vessel
30	chr6:106997800-107008400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:106998000-107004000	Strong transcription	NHEK	skin
32	chr6:106998000-107005600	Strong transcription	HMEC	breast
33	chr6:106998000-107007000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr6:106998200-107005600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr6:106999000-107022400	Weak transcription	Right Ventricle	heart
36	chr6:106999200-107022400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr6:106999400-107004000	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr6:106999600-107004000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr6:106999600-107005600	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr6:106999800-107030600	Weak transcription	H9 Cell Line	embryonic stem cell
41	chr6:107000200-107004000	Strong transcription	Esophagus	oesophagus
42	chr6:107000200-107004200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr6:107000400-107004800	Strong transcription	Dnd41	blood
44	chr6:107000400-107018800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:107000800-107004000	Strong transcription	Adipose Nuclei	Adipose
46	chr6:107000800-107004200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr6:107000800-107004200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr6:107000800-107004200	Strong transcription	Liver	Liver
49	chr6:107000800-107021200	Strong transcription	Primary B cells from cord blood	blood
50	chr6:107001000-107004000	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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