Variant report

Variant	rs10779564
Chromosome Location	chr1:211809449-211809450
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:10)
CpG islands
(count:0)
Chromatin interactive
region (count:3)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:10 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:211809178-211809508	MCF10A-Er-Src	breast:	n/a	n/a
2	SMARCC1	chr1:211809200-211810986	Hela-S3	cervix:	n/a	n/a
3	GTF3C2	chr1:211808656-211810403	Hela-S3	cervix:	n/a	n/a
4	CEBPB	chr1:211809165-211809572	IMR90	lung:	n/a	n/a
5	STAT3	chr1:211809170-211809490	MCF10A-Er-Src	breast:	n/a	n/a
6	CEBPB	chr1:211809217-211809545	A549	lung:	n/a	n/a
7	SMARCB1	chr1:211809353-211810640	Hela-S3	cervix:	n/a	n/a
8	STAT3	chr1:211809108-211809482	MCF10A-Er-Src	breast:	n/a	n/a
9	CEBPB	chr1:211809083-211809560	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr1:211809351-211809580	Hela-S3	cervix:	n/a	n/a

No data

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:211805499..211810389-chr1:211816053..211819078,4	K562	blood:
2	chr1:211808019..211810498-chr1:211819976..211822363,2	K562	blood:
3	chr1:211788189..211791176-chr1:211807791..211810721,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRAF5-4	chr1:211809248-211809787	XLOC_000549
2	lnc-NEK2-1	chr1:211809248-211809787	ENSG00000228792.2

No data

Variant related genes	Relation type
ENSG00000227764	TF binding region
ENSG00000228792	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10158305	0.84[EUR][1000 genomes]
rs10158307	0.83[EUR][1000 genomes]
rs10158309	0.84[EUR][1000 genomes]
rs10158749	0.84[EUR][1000 genomes]
rs10158790	0.84[EUR][1000 genomes]
rs10158874	0.84[EUR][1000 genomes]
rs10159253	0.84[EUR][1000 genomes]
rs10779565	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10779566	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863919	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10863920	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119780	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11119785	0.85[JPT][hapmap]
rs11119786	0.86[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs11119787	0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11576789	0.87[CEU][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs11577255	0.80[EUR][1000 genomes]
rs12087826	0.87[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12090722	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12123429	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12142250	0.84[EUR][1000 genomes]
rs12727505	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12741252	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12758005	0.87[CEU][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs1373293	0.84[EUR][1000 genomes]
rs35531215	0.82[EUR][1000 genomes]
rs4245741	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4951415	0.91[ASN][1000 genomes]
rs4951416	0.91[CEU][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951418	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951419	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951420	0.82[CHB][hapmap]
rs4951421	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951537	0.84[JPT][hapmap];0.84[ASN][1000 genomes]
rs4951539	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4951540	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61851777	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6540697	0.80[AMR][1000 genomes]
rs6540698	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6660850	0.80[AMR][1000 genomes]
rs6669878	0.84[EUR][1000 genomes]
rs6670986	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671497	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6671506	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6675796	0.82[CEU][hapmap]
rs6682640	0.84[AMR][1000 genomes]
rs7513348	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7523748	0.92[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.96[LWK][hapmap];0.91[MEX][hapmap];0.96[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7551699	0.80[EUR][1000 genomes]
rs894853	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs894854	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs894855	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv1010919	chr1:211804252-211823073	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:211804200-211813400	Weak transcription	H1 Cell Line	embryonic stem cell
2	chr1:211804200-211816600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:211806800-211809600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr1:211806800-211809600	Weak transcription	Fetal Intestine Small	intestine
5	chr1:211806800-211811600	Weak transcription	Fetal Intestine Large	intestine
6	chr1:211806800-211813000	Weak transcription	Stomach Mucosa	stomach
7	chr1:211807000-211809600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:211807000-211810600	Weak transcription	Placenta	Placenta
9	chr1:211807000-211811600	Weak transcription	Esophagus	oesophagus
10	chr1:211807000-211812000	Weak transcription	Adipose Nuclei	Adipose
11	chr1:211807000-211816200	Weak transcription	Colonic Mucosa	Colon
12	chr1:211807000-211816200	Weak transcription	Ovary	ovary
13	chr1:211807200-211809600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr1:211807200-211809800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr1:211807200-211812000	Weak transcription	NHLF	lung
16	chr1:211807200-211816600	Weak transcription	Right Ventricle	heart
17	chr1:211807200-211817200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:211807400-211810000	Weak transcription	Spleen	Spleen
19	chr1:211807400-211812200	Weak transcription	NH-A	brain
20	chr1:211807400-211816800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:211807600-211811600	Weak transcription	Liver	Liver
22	chr1:211807600-211812800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr1:211807600-211812800	Weak transcription	Pancreas	Pancrea
24	chr1:211807600-211813000	Weak transcription	HSMMtube	muscle
25	chr1:211807600-211816600	Weak transcription	Left Ventricle	heart
26	chr1:211807800-211809600	Weak transcription	HMEC	breast
27	chr1:211808000-211810000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:211808600-211810800	Enhancers	Osteobl	bone
29	chr1:211808800-211810600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr1:211809200-211810200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr1:211809200-211810400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr1:211809400-211809800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr1:211809400-211809800	Flanking Active TSS	Hela-S3	cervix
34	chr1:211809400-211810200	Enhancers	HSMM	muscle
35	chr1:211809400-211810200	Enhancers	NHDF-Ad	bronchial
36	chr1:211809400-211810800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr1:211809400-211810800	Enhancers	Muscle Satellite Cultured Cells	--
38	chr1:211809400-211810800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:211809400-211811200	Enhancers	HepG2	liver
40	chr1:211809400-211813000	Enhancers	A549	lung

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