Variant report

Variant	rs664721
Chromosome Location	chr6:144599875-144599876
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	chr6:144597562..144600521-chr6:144605726..144607398,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000152818	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs2473129	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2502621	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs583341	1.00[CEU][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs583788	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs584283	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586016	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586471	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs586553	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs587691	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs587889	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs589892	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs590329	0.85[ASN][1000 genomes]
rs590362	0.85[ASN][1000 genomes]
rs591311	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs592388	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs592667	0.88[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs598222	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs599074	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs601816	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs601873	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs602764	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs603692	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs612928	1.00[CEU][hapmap];0.83[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs615755	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs616619	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs619750	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs623320	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs632972	0.91[EUR][1000 genomes]
rs633106	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs633802	0.92[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs643596	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs644124	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs646837	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs647282	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs649426	0.96[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs652262	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs652765	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs658562	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs659899	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs660286	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs660307	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs660770	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs662419	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs664541	0.93[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs665135	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs667740	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs667765	1.00[CEU][hapmap];0.92[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs672468	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs676859	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs680093	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs681854	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs681916	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs682704	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74671	0.84[EUR][1000 genomes]
rs849661	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830831	chr6:144501371-144649509	Bivalent/Poised TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs664721	RP1-83M4.2	cis	Nerve Tibial	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144587800-144605000	Weak transcription	Right Atrium	heart
2	chr6:144587800-144605800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr6:144598400-144600400	Enhancers	Liver	Liver
4	chr6:144598600-144600400	Enhancers	Adipose Nuclei	Adipose
5	chr6:144599200-144600000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr6:144599200-144600400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr6:144599200-144600400	Enhancers	NHEK	skin
8	chr6:144599200-144600600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:144599200-144601000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:144599200-144605000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr6:144599600-144600200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:144599600-144600400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:144599600-144600400	Enhancers	Hela-S3	cervix
14	chr6:144599600-144600800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:144599600-144601000	Enhancers	HMEC	breast
16	chr6:144599600-144601400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:144599600-144601400	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr6:144599600-144601600	Enhancers	H9 Cell Line	embryonic stem cell
19	chr6:144599800-144600000	Enhancers	iPS-20b Cell Line	embryonic stem cell
20	chr6:144599800-144600200	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
21	chr6:144599800-144600200	Enhancers	Placenta	Placenta
22	chr6:144599800-144600200	Enhancers	Pancreas	Pancrea
23	chr6:144599800-144600200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr6:144599800-144600200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr6:144599800-144600200	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr6:144599800-144600200	Enhancers	A549	lung
27	chr6:144599800-144600400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:144599800-144600400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr6:144599800-144600600	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr6:144599800-144600800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr6:144599800-144601200	Enhancers	ES-I3 Cell Line	embryonic stem cell
32	chr6:144599800-144601200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr6:144599800-144601200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr6:144599800-144601200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr6:144599800-144601400	Enhancers	H1 Cell Line	embryonic stem cell
36	chr6:144599800-144601400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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