Variant report

Variant	rs61425457
Chromosome Location	chr1:94276227-94276228
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	chr1:94146662..94149106-chr1:94275928..94279554,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10489605	0.83[ASN][1000 genomes]
rs10874795	0.97[ASN][1000 genomes]
rs1108527	0.81[EUR][1000 genomes]
rs1108528	0.86[EUR][1000 genomes]
rs11164994	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11165001	0.91[ASN][1000 genomes]
rs11165019	0.97[ASN][1000 genomes]
rs12079584	0.97[ASN][1000 genomes]
rs12239830	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17100397	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17110408	0.91[ASN][1000 genomes]
rs17304770	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17878271	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17878294	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17881810	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17884788	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17885151	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17886352	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1877605	0.89[EUR][1000 genomes]
rs2223908	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3761913	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs41292665	0.90[EUR][1000 genomes]
rs4615846	0.82[ASN][1000 genomes]
rs57870303	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781048	0.85[EUR][1000 genomes]
rs61781049	0.94[EUR][1000 genomes]
rs61781051	1.00[EUR][1000 genomes]
rs61781053	0.98[EUR][1000 genomes]
rs61781054	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781055	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781056	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61781057	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782162	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782163	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782164	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782165	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782398	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782399	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782400	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782404	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782405	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782410	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782413	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782449	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61782450	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61782451	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61782458	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61782459	0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6660794	0.91[ASN][1000 genomes]
rs6671839	0.91[ASN][1000 genomes]
rs6674149	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6689215	0.89[ASN][1000 genomes]
rs6689746	0.91[ASN][1000 genomes]
rs6703468	0.91[ASN][1000 genomes]
rs717913	0.91[ASN][1000 genomes]
rs72723114	1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723118	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723125	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723138	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723157	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723165	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72723169	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72723178	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72967397	0.97[ASN][1000 genomes]
rs7523682	0.94[EUR][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	nsv546822	chr1:94246577-94289863	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	esv1815663	chr1:94246577-94291252	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv1877	chr1:94247756-94292908	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv508415	chr1:94256122-94305339	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1802380	chr1:94272119-94291252	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61425457	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94271000-94279200	Weak transcription	Adipose Nuclei	Adipose
2	chr1:94271200-94276600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr1:94271200-94276600	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:94271200-94278200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:94273600-94278600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:94273600-94282800	Weak transcription	Lung	lung
7	chr1:94274200-94278200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr1:94274800-94279400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr1:94275400-94279600	Enhancers	NHDF-Ad	bronchial
10	chr1:94275400-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:94275400-94281400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:94275600-94277600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:94275800-94276600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:94275800-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr1:94275800-94282400	Enhancers	Muscle Satellite Cultured Cells	--
16	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
17	chr1:94275800-94285000	Enhancers	HMEC	breast
18	chr1:94276000-94276400	Enhancers	NHLF	lung
19	chr1:94276000-94277400	Enhancers	Osteobl	bone
20	chr1:94276000-94277600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:94276000-94278200	Enhancers	Right Atrium	heart
22	chr1:94276000-94278600	Enhancers	Fetal Lung	lung
23	chr1:94276000-94281400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:94276000-94283600	Enhancers	HSMM	muscle
25	chr1:94276000-94285200	Enhancers	Placenta	Placenta
26	chr1:94276200-94276600	Weak transcription	Right Ventricle	heart
27	chr1:94276200-94277000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr1:94276200-94277600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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