Variant report

Variant	rs3792128
Chromosome Location	chr2:100213966-100213967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100212449..100215580-chr2:100217291..100220527,3	K562	blood:
2	chr2:100210702..100213204-chr2:100213341..100216130,3	MCF-7	breast:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11123789	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11895560	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11900988	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11901863	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12474603	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12612124	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12616127	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12712052	0.81[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2309728	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34112064	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4568000	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4850908	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55989048	0.82[ASN][1000 genomes]
rs6716694	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6722898	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7558495	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7561197	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7561948	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7567996	0.82[EUR][1000 genomes]
rs9973326	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9973472	0.81[AMR][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	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3792128	LYG1	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100162800-100219200	Strong transcription	Primary B cells from peripheral blood	blood
2	chr2:100186800-100214600	Weak transcription	Fetal Intestine Small	intestine
3	chr2:100190400-100218200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:100191400-100215000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:100198400-100214800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:100199400-100217800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr2:100202600-100214000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:100203000-100216000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:100203200-100215200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr2:100203200-100221400	Weak transcription	Rectal Smooth Muscle	rectum
11	chr2:100203400-100221200	Weak transcription	Colon Smooth Muscle	Colon
12	chr2:100203800-100217200	Weak transcription	Liver	Liver
13	chr2:100204000-100217400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:100204000-100218000	Weak transcription	Fetal Lung	lung
15	chr2:100204000-100221800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:100207800-100219800	Strong transcription	Primary B cells from cord blood	blood
17	chr2:100210200-100215000	Weak transcription	Fetal Thymus	thymus
18	chr2:100210400-100218400	Weak transcription	Dnd41	blood
19	chr2:100210400-100219800	Weak transcription	Gastric	stomach
20	chr2:100210600-100215000	Weak transcription	Lung	lung
21	chr2:100210600-100217600	Weak transcription	Spleen	Spleen
22	chr2:100210600-100224200	Weak transcription	Brain Germinal Matrix	brain
23	chr2:100210800-100216800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
24	chr2:100211000-100219000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:100211000-100234200	Weak transcription	Thymus	Thymus
26	chr2:100211000-100249600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr2:100211600-100215000	Weak transcription	Fetal Kidney	kidney
28	chr2:100211600-100219800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr2:100212400-100215400	Strong transcription	Primary T cells from cord blood	blood
30	chr2:100212800-100221400	Weak transcription	Ovary	ovary
31	chr2:100213000-100218000	Weak transcription	Fetal Brain Female	brain
32	chr2:100213200-100216800	Weak transcription	Fetal Brain Male	brain
33	chr2:100213400-100214200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr2:100213400-100215000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:100213600-100214800	Enhancers	NH-A	brain
36	chr2:100213600-100214800	Enhancers	Osteobl	bone
37	chr2:100213600-100215000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:100213800-100214800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr2:100213800-100215200	Enhancers	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links