Variant report

Variant	rs698927
Chromosome Location	chr1:93836218-93836219
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:93835221..93837271-chr1:93838238..93840326,2	MCF-7	breast:

Extended variants
information (count: 111 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10443193	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10782959	0.90[CHD][hapmap]
rs1081522	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10874783	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10874784	0.91[EUR][1000 genomes]
rs11164879	0.90[CHB][hapmap]
rs11164885	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11164897	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11164905	0.82[ASN][1000 genomes]
rs11164908	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11164921	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11576494	0.80[ASN][1000 genomes]
rs12030549	0.91[CHB][hapmap]
rs12030843	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12031709	0.87[AFR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12031765	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12033147	0.94[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs12036057	0.82[ASN][1000 genomes]
rs12044557	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12044883	0.83[CHB][hapmap];0.81[ASN][1000 genomes]
rs12048219	0.81[ASN][1000 genomes]
rs12118262	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs12133576	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs12138486	0.87[CEU][hapmap];0.87[CHD][hapmap]
rs12405487	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12406245	0.91[CHB][hapmap]
rs12563120	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12566752	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12752223	0.81[ASN][1000 genomes]
rs1335679	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs1365297	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1426318	0.91[CHB][hapmap]
rs1559828	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs2031225	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs2031226	0.89[CHB][hapmap]
rs2114271	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2114272	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2162276	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2255722	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs2296558	0.90[CHB][hapmap]
rs2391251	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2391254	0.91[CHB][hapmap];0.94[JPT][hapmap]
rs2484486	0.90[CHB][hapmap];0.87[CHD][hapmap];0.83[JPT][hapmap]
rs2765545	0.85[CHB][hapmap];0.97[CHD][hapmap]
rs2783495	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs2783499	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.87[TSI][hapmap]
rs2783500	0.93[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs2783501	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs3087457	0.84[ASN][1000 genomes]
rs35628716	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35910103	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35915989	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3754186	0.91[CHB][hapmap]
rs3767962	0.81[ASN][1000 genomes]
rs3767964	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs3904665	0.83[CHB][hapmap];0.93[JPT][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3904666	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap]
rs4000699	0.91[CHB][hapmap]
rs4240966	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs4484937	1.00[ASW][hapmap];0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.97[MKK][hapmap];0.84[TSI][hapmap];0.82[ASN][1000 genomes]
rs4847240	0.91[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.81[ASN][1000 genomes]
rs4847241	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4847242	1.00[CEU][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap];0.84[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4847408	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs4847412	0.81[ASN][1000 genomes]
rs4847426	0.92[EUR][1000 genomes]
rs531358	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs58354545	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs612037	0.91[CHB][hapmap]
rs61266405	0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61799500	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61799516	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61799538	0.82[ASN][1000 genomes]
rs622608	0.90[CHB][hapmap]
rs637646	0.89[CHB][hapmap]
rs6541349	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6541401	0.91[CHB][hapmap]
rs6541404	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs6658257	0.81[ASN][1000 genomes]
rs6676902	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6680022	0.81[ASN][1000 genomes]
rs6682670	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs6684908	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6691545	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6694508	0.81[ASN][1000 genomes]
rs6703310	0.91[CHB][hapmap];1.00[CHD][hapmap]
rs687394	0.91[CEU][hapmap];0.89[CHB][hapmap]
rs693737	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs72959220	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7513705	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7517363	0.90[CHB][hapmap];1.00[CHD][hapmap]
rs7525248	0.90[CHB][hapmap];0.81[ASN][1000 genomes]
rs7535628	0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap]
rs7539307	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs771454	0.87[ASN][1000 genomes]
rs771458	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771461	0.87[ASN][1000 genomes]
rs771462	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs771465	0.87[ASN][1000 genomes]
rs771470	0.81[ASN][1000 genomes]
rs771476	0.83[ASN][1000 genomes]
rs771478	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs771479	0.84[ASN][1000 genomes]
rs771481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs771482	0.84[ASN][1000 genomes]
rs797668	0.91[CHB][hapmap]
rs797680	0.91[CHB][hapmap]
rs810027	0.90[CHB][hapmap];0.90[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs812214	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs942196	0.91[CHB][hapmap]

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	nsv871640	chr1:93807122-93953469	Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs698927	OSTF1	trans	parietal	SCAN
rs698927	GBP5	cis	parietal	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:93813400-93840000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr1:93813400-93840400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:93815400-93839800	Weak transcription	Aorta	Aorta
4	chr1:93816600-93841800	Weak transcription	Brain Cingulate Gyrus	brain
5	chr1:93816800-93841200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:93818800-93837200	Weak transcription	Fetal Kidney	kidney
7	chr1:93820600-93837200	Weak transcription	Colonic Mucosa	Colon
8	chr1:93821000-93838800	Weak transcription	Ovary	ovary
9	chr1:93822200-93840200	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr1:93824200-93838200	Weak transcription	Pancreas	Pancrea
11	chr1:93824200-93839400	Weak transcription	Lung	lung
12	chr1:93824200-93839800	Weak transcription	Fetal Brain Female	brain
13	chr1:93824200-93840000	Weak transcription	Right Ventricle	heart
14	chr1:93824200-93841000	Weak transcription	Brain Germinal Matrix	brain
15	chr1:93824200-93841000	Weak transcription	Spleen	Spleen
16	chr1:93824400-93839400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:93824400-93839400	Weak transcription	Brain Anterior Caudate	brain
18	chr1:93824400-93842000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:93824600-93838200	Weak transcription	Fetal Heart	heart
20	chr1:93824600-93840000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:93825200-93840800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:93825400-93840600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr1:93825600-93839400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr1:93826200-93841400	Weak transcription	Brain Hippocampus Middle	brain
25	chr1:93828200-93842400	Weak transcription	Primary hematopoietic stem cells	blood
26	chr1:93829200-93843600	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:93829800-93839400	Weak transcription	Adipose Nuclei	Adipose
28	chr1:93830400-93836600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:93831400-93836800	Weak transcription	Hela-S3	cervix
30	chr1:93831600-93837600	Weak transcription	HMEC	breast
31	chr1:93831600-93839200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:93831600-93841000	Weak transcription	NHEK	skin
33	chr1:93831800-93836800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr1:93831800-93838000	Weak transcription	NH-A	brain
35	chr1:93831800-93840600	Weak transcription	A549	lung
36	chr1:93832400-93840000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr1:93832600-93839800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr1:93833200-93837800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr1:93833200-93838200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:93833200-93839400	Weak transcription	Esophagus	oesophagus
41	chr1:93833200-93839400	Weak transcription	Left Ventricle	heart
42	chr1:93833200-93839800	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr1:93833200-93841200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:93833200-93841200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr1:93833200-93841400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr1:93833400-93837600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr1:93833400-93838000	Weak transcription	Osteobl	bone
48	chr1:93833400-93839400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr1:93833400-93839600	Weak transcription	Fetal Muscle Trunk	muscle
50	chr1:93833400-93840000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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