Variant report

Variant	rs1687947
Chromosome Location	chr1:94711524-94711525
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr1:94711510-94711944	MCF10A-Er-Src	breast:	n/a	chr1:94711794-94711815
2	POLR2A	chr1:94710437-94711876	HUVEC	blood vessel:	n/a	n/a
3	STAT3	chr1:94711361-94711978	MCF10A-Er-Src	breast:	n/a	chr1:94711794-94711815
4	STAT3	chr1:94711148-94711931	MCF10A-Er-Src	breast:	n/a	chr1:94711794-94711815
5	POLR2A	chr1:94710886-94713722	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr1:94711220-94713680	HUVEC	blood vessel:	n/a	n/a
7	POLR2A	chr1:94710334-94714607	PANC-1	pancreas:	n/a	n/a
8	POLR2A	chr1:94710993-94713638	HUVEC	blood vessel:	n/a	n/a
9	STAT3	chr1:94711510-94711940	MCF10A-Er-Src	breast:	n/a	chr1:94711794-94711815
10	MYC	chr1:94711365-94711700	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr1:94710879-94711777	HCT-116	colon:	n/a	n/a
12	POLR2A	chr1:94710704-94713682	HUVEC	blood vessel:	n/a	n/a
13	POLR2A	chr1:94710307-94712948	PANC-1	pancreas:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:94701840..94705805-chr1:94711160..94713439,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231363	TF binding region
ENSG00000137962	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1054626	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11165103	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165114	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12022859	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs12024941	0.87[EUR][1000 genomes]
rs12027548	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12031606	0.87[EUR][1000 genomes]
rs12036085	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12038745	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039546	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12042509	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12046536	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12093742	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12562103	0.91[EUR][1000 genomes]
rs12563826	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1360365	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576592	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1611832	0.88[EUR][1000 genomes]
rs1622451	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1623248	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1623314	1.00[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1629275	0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1687950	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928	1.00[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17111408	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17111419	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17111426	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17111436	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1765636	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1765640	1.00[CEU][hapmap];0.80[CHB][hapmap];0.84[JPT][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1929131	0.86[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1999270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1999271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2130899	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2391472	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35275815	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789690	0.89[EUR][1000 genomes]
rs4543802	0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4847201	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4847296	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55961421	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56037795	0.87[EUR][1000 genomes]
rs57666908	0.89[EUR][1000 genomes]
rs6541343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6541345	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6662877	0.90[EUR][1000 genomes]
rs6673491	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6675959	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6681827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66918029	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66961454	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67180557	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67554381	0.88[EUR][1000 genomes]
rs67612304	0.91[EUR][1000 genomes]
rs67681803	0.87[EUR][1000 genomes]
rs67807923	0.90[EUR][1000 genomes]
rs68193246	0.91[EUR][1000 genomes]
rs7413345	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7415246	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7515965	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7520754	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7525320	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7533977	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7554714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[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	nsv428510	chr1:94709575-94866655	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94703600-94712000	Weak transcription	HSMM	muscle
2	chr1:94709000-94712200	Enhancers	Liver	Liver
3	chr1:94709800-94711600	Flanking Active TSS	NHEK	skin
4	chr1:94709800-94712400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:94709800-94712800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr1:94709800-94713600	Active TSS	Right Atrium	heart
7	chr1:94710000-94711600	Enhancers	A549	lung
8	chr1:94710000-94713600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:94710600-94711600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr1:94710600-94712200	Active TSS	Adipose Nuclei	Adipose
11	chr1:94710600-94712200	Enhancers	HepG2	liver
12	chr1:94710800-94711600	Flanking Active TSS	Osteobl	bone
13	chr1:94711000-94711600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:94711000-94711800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr1:94711000-94711800	Flanking Active TSS	HUVEC	blood vessel
16	chr1:94711000-94712400	Active TSS	Skeletal Muscle Male	skeletal muscle
17	chr1:94711000-94713400	Active TSS	Muscle Satellite Cultured Cells	--
18	chr1:94711000-94713800	Active TSS	Psoas Muscle	Psoas
19	chr1:94711200-94711600	Flanking Active TSS	NHDF-Ad	bronchial
20	chr1:94711200-94711800	Flanking Active TSS	HMEC	breast
21	chr1:94711200-94711800	Flanking Active TSS	NH-A	brain
22	chr1:94711200-94712200	Active TSS	Fetal Muscle Leg	muscle
23	chr1:94711200-94713800	Active TSS	Left Ventricle	heart
24	chr1:94711200-94713800	Active TSS	Right Ventricle	heart
25	chr1:94711400-94711600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr1:94711400-94711600	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:94711400-94711600	Bivalent Enhancer	Fetal Lung	lung
28	chr1:94711400-94711800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr1:94711400-94711800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
30	chr1:94711400-94711800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr1:94711400-94711800	Flanking Active TSS	NHLF	lung
32	chr1:94711400-94712200	Active TSS	Fetal Adrenal Gland	Adrenal Gland
33	chr1:94711400-94712200	Active TSS	Fetal Stomach	stomach
34	chr1:94711400-94712200	Enhancers	Placenta Amnion	Placenta Amnion
35	chr1:94711400-94713000	Bivalent/Poised TSS	Fetal Kidney	kidney
36	chr1:94711400-94713600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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