Variant report

Variant	rs57360378
Chromosome Location	chr2:20786133-20786134
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:20783319..20786192-chr2:20833674..20835720,2	MCF-7	breast:
2	chr2:20645526..20651779-chr2:20782666..20787622,12	MCF-7	breast:
3	chr2:20783982..20787771-chr2:20790367..20794656,9	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GDF7-4	chr2:20786008-20786446	NONHSAT069453
2	lnc-C2orf43-6	chr2:20786008-20786446	ENSG00000269976.1

Variant related genes	Relation type
ENSG00000228950	Chromatin interaction
ENSG00000143878	Chromatin interaction
ENSG00000231948	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs28488411	0.88[AFR][1000 genomes]
rs28529647	0.88[AFR][1000 genomes]
rs28600892	0.88[AFR][1000 genomes]
rs28642817	0.88[AFR][1000 genomes]
rs55793738	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58726406	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59300971	0.86[AFR][1000 genomes]
rs59618840	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59771803	0.93[AFR][1000 genomes]
rs60631754	0.81[EUR][1000 genomes]
rs60759855	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61272752	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62124220	0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62124225	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124226	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124227	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124228	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124229	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124230	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124231	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124232	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62124234	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62125670	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62125672	0.81[EUR][1000 genomes]
rs73916905	0.90[EUR][1000 genomes]
rs73919913	0.85[AFR][1000 genomes]
rs73919915	0.87[AFR][1000 genomes]
rs73919918	0.91[AFR][1000 genomes]
rs73919920	0.93[AFR][1000 genomes]
rs73919921	0.93[AFR][1000 genomes]
rs73919922	0.93[AFR][1000 genomes]
rs73919923	0.92[AFR][1000 genomes]
rs73919924	0.93[AFR][1000 genomes]
rs73919926	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73919928	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73919930	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7564684	0.93[AFR][1000 genomes]
rs7574045	0.93[AFR][1000 genomes]
rs7574289	0.81[AFR][1000 genomes]
rs7588678	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7595132	0.82[AFR][1000 genomes]
rs7601273	0.93[AFR][1000 genomes]
rs896737	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833537	chr2:20630092-20826816	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv833548	chr2:20682073-20864078	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1012037	chr2:20770850-20824893	Strong transcription Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535598	chr2:20770850-20824893	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20765800-20786200	Enhancers	HUVEC	blood vessel
2	chr2:20781800-20786200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr2:20781800-20786800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr2:20782000-20786200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:20782000-20786200	Enhancers	Fetal Intestine Small	intestine
6	chr2:20782000-20787400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr2:20782200-20786200	Enhancers	Placenta	Placenta
8	chr2:20782200-20786400	Enhancers	Fetal Stomach	stomach
9	chr2:20782400-20786400	Enhancers	Right Atrium	heart
10	chr2:20782400-20786400	Enhancers	Skeletal Muscle Female	skeletal muscle
11	chr2:20782600-20787800	Enhancers	Adipose Nuclei	Adipose
12	chr2:20782800-20786200	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr2:20782800-20787400	Enhancers	Fetal Muscle Leg	muscle
14	chr2:20783400-20786800	Enhancers	NHDF-Ad	bronchial
15	chr2:20783800-20786200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:20783800-20786200	Enhancers	Ovary	ovary
17	chr2:20784000-20786400	Flanking Active TSS	HepG2	liver
18	chr2:20784200-20786200	Enhancers	Psoas Muscle	Psoas
19	chr2:20784400-20786600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:20784600-20794200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr2:20784800-20786200	Enhancers	Colon Smooth Muscle	Colon
22	chr2:20784800-20786200	Enhancers	NHLF	lung
23	chr2:20785000-20786200	Enhancers	Duodenum Mucosa	Duodenum
24	chr2:20785000-20786200	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:20785000-20786200	Enhancers	Stomach Smooth Muscle	stomach
26	chr2:20785000-20786400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr2:20785000-20787200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr2:20785000-20788800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:20785000-20796000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr2:20785200-20788800	Weak transcription	HSMM	muscle
31	chr2:20785200-20789000	Weak transcription	NHEK	skin
32	chr2:20785200-20789200	Weak transcription	Osteobl	bone
33	chr2:20785400-20788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr2:20785400-20788600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr2:20785400-20789200	Weak transcription	HMEC	breast
36	chr2:20785400-20789200	Weak transcription	HSMMtube	muscle
37	chr2:20785400-20789400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr2:20785600-20787200	Weak transcription	Fetal Kidney	kidney
39	chr2:20785600-20788800	Weak transcription	NH-A	brain
40	chr2:20785600-20790200	Weak transcription	Fetal Intestine Large	intestine
41	chr2:20785800-20786400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr2:20785800-20786400	Enhancers	Fetal Muscle Trunk	muscle
43	chr2:20785800-20786600	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr2:20785800-20787000	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr2:20785800-20787000	Weak transcription	Brain Angular Gyrus	brain
46	chr2:20785800-20787000	Weak transcription	K562	blood
47	chr2:20785800-20788400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr2:20785800-20789800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr2:20785800-20790200	Weak transcription	Fetal Heart	heart
50	chr2:20785800-20790600	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links