Variant report

Variant	rs6701929
Chromosome Location	chr1:172238885-172238886
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:172238202..172240492-chr1:172241261..172243973,2	MCF-7	breast:
2	chr1:172237804..172239793-chr1:172244110..172246344,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10489289	0.83[CHD][hapmap]
rs10489290	0.83[CHD][hapmap]
rs10911387	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11808940	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12049422	0.93[CEU][hapmap];0.94[GIH][hapmap];0.85[MEX][hapmap]
rs12069167	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs12075079	0.83[CHD][hapmap]
rs12082431	0.82[CHD][hapmap]
rs2289635	0.83[CHD][hapmap]
rs2586389	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2586392	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2586394	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2586401	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586403	0.93[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586404	0.93[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586407	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586408	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586410	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586411	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2586412	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2586413	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2757493	0.93[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2757495	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2757496	0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3850640	0.80[CHD][hapmap]
rs4072117	0.83[CHD][hapmap]
rs4382763	0.82[CHD][hapmap]
rs477289	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs479336	1.00[CEU][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.93[EUR][1000 genomes]
rs6678749	0.83[CHD][hapmap]
rs7550558	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9425545	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv465650	chr1:172175115-172247127	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv548192	chr1:172175115-172247127	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6701929	F5	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172225600-172246600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:172235000-172239800	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:172236200-172247000	Weak transcription	Muscle Satellite Cultured Cells	--
4	chr1:172237800-172239400	Flanking Active TSS	A549	lung
5	chr1:172237800-172239600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:172238000-172239200	Enhancers	HUES64 Cell Line	embryonic stem cell
7	chr1:172238000-172239200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr1:172238000-172239200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr1:172238000-172239400	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:172238000-172240400	Enhancers	Osteobl	bone
11	chr1:172238200-172239200	Flanking Active TSS	HepG2	liver
12	chr1:172238200-172239600	Enhancers	NHDF-Ad	bronchial
13	chr1:172238200-172239800	Enhancers	ES-I3 Cell Line	embryonic stem cell
14	chr1:172238200-172240200	Enhancers	Rectal Smooth Muscle	rectum
15	chr1:172238200-172240400	Enhancers	Fetal Lung	lung
16	chr1:172238400-172239000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:172238400-172239000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr1:172238400-172239000	Enhancers	Fetal Muscle Leg	muscle
19	chr1:172238400-172239000	Enhancers	Ovary	ovary
20	chr1:172238400-172239000	Enhancers	Pancreas	Pancrea
21	chr1:172238400-172239400	Enhancers	Hela-S3	cervix
22	chr1:172238600-172239200	Enhancers	iPS-20b Cell Line	embryonic stem cell
23	chr1:172238600-172239600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr1:172238600-172240000	Enhancers	Fetal Heart	heart
25	chr1:172238600-172241600	Weak transcription	Brain Substantia Nigra	brain
26	chr1:172238800-172239000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:172238800-172239000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:172238800-172239000	Enhancers	Fetal Stomach	stomach
29	chr1:172238800-172239000	Enhancers	Placenta Amnion	Placenta Amnion
30	chr1:172238800-172239000	Enhancers	NH-A	brain
31	chr1:172238800-172239200	Enhancers	Colon Smooth Muscle	Colon
32	chr1:172238800-172239200	Enhancers	Stomach Mucosa	stomach
33	chr1:172238800-172239600	Enhancers	Stomach Smooth Muscle	stomach
34	chr1:172238800-172239600	Enhancers	GM12878-XiMat	blood
35	chr1:172238800-172239800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:172238800-172239800	Weak transcription	Brain Anterior Caudate	brain
37	chr1:172238800-172240400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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