Variant report

Variant	rs61782403
Chromosome Location	chr1:94278255-94278256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94146662..94149106-chr1:94275928..94279554,4	MCF-7	breast:
2	chr1:94093897..94096295-chr1:94277751..94279857,3	MCF-7	breast:
3	chr1:94146643..94149409-chr1:94276998..94280390,3	MCF-7	breast:
4	chr1:94137739..94141828-chr1:94278104..94280351,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137936	Chromatin interaction

Extended variants
information (count: 72 )
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]
rs61425457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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]
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:6 , 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
6	esv1822452	chr1:94278128-94320233	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	121 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61782403	GCLM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94271000-94279200	Weak transcription	Adipose Nuclei	Adipose
2	chr1:94273600-94278600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:94273600-94282800	Weak transcription	Lung	lung
4	chr1:94274800-94279400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr1:94275400-94279600	Enhancers	NHDF-Ad	bronchial
6	chr1:94275400-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr1:94275400-94281400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:94275800-94280200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr1:94275800-94282400	Enhancers	Muscle Satellite Cultured Cells	--
10	chr1:94275800-94284200	Enhancers	Hela-S3	cervix
11	chr1:94275800-94285000	Enhancers	HMEC	breast
12	chr1:94276000-94278600	Enhancers	Fetal Lung	lung
13	chr1:94276000-94281400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:94276000-94283600	Enhancers	HSMM	muscle
15	chr1:94276000-94285200	Enhancers	Placenta	Placenta
16	chr1:94276400-94278600	Weak transcription	NHLF	lung
17	chr1:94276600-94278800	Enhancers	Left Ventricle	heart
18	chr1:94276800-94283800	Enhancers	NHEK	skin
19	chr1:94277000-94282400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr1:94277000-94284400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr1:94277000-94285000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr1:94277200-94278600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr1:94277200-94280000	Weak transcription	Fetal Brain Female	brain
24	chr1:94277200-94282600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:94277400-94278600	Weak transcription	Osteobl	bone
26	chr1:94277400-94278800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr1:94277400-94278800	Weak transcription	HSMMtube	muscle
28	chr1:94277400-94278800	Weak transcription	NH-A	brain
29	chr1:94277400-94279400	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:94277600-94278600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:94277600-94278600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr1:94277600-94279400	Weak transcription	HUVEC	blood vessel
33	chr1:94277600-94284600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:94277800-94279600	Weak transcription	Fetal Kidney	kidney
35	chr1:94277800-94282600	Weak transcription	Fetal Stomach	stomach
36	chr1:94278000-94279200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:94278000-94279800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr1:94278000-94279800	Enhancers	HepG2	liver
39	chr1:94278000-94280000	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr1:94278200-94279000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr1:94278200-94279200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr1:94278200-94279800	Weak transcription	Fetal Brain Male	brain
43	chr1:94278200-94279800	Weak transcription	Fetal Muscle Leg	muscle
44	chr1:94278200-94279800	Weak transcription	Right Atrium	heart
45	chr1:94278200-94281600	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:94278200-94282600	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr1:94278200-94282800	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links