Variant report

Variant	rs828852
Chromosome Location	chr2:74383911-74383912
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	chr2:74366917..74386173-chr2:74421816..74431613,38	K562	blood:
2	chr2:74382240..74383981-chr2:74386792..74388398,2	K562	blood:

Variant related genes	Relation type
ENSG00000065911	Chromatin interaction

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

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

rs_ID	r²[population]
rs1056528	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1095966	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1095967	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12469365	0.83[EUR][1000 genomes]
rs1667600	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1667610	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1667627	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.87[MEX][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3108163	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3108165	0.83[EUR][1000 genomes]
rs4630794	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs702465	0.92[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828860	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828861	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828874	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs828875	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs828887	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.87[MEX][hapmap];0.88[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828891	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs828893	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs844168	0.81[CEU][hapmap]
rs844169	0.87[EUR][1000 genomes]
rs860455	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs828852	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74375800-74391200	Weak transcription	Aorta	Aorta
2	chr2:74375800-74403600	Weak transcription	Stomach Mucosa	stomach
3	chr2:74376000-74384000	Weak transcription	Fetal Intestine Small	intestine
4	chr2:74376000-74384000	Weak transcription	Small Intestine	intestine
5	chr2:74376000-74384200	Weak transcription	Esophagus	oesophagus
6	chr2:74376000-74384200	Weak transcription	Right Ventricle	heart
7	chr2:74376000-74385600	Weak transcription	Gastric	stomach
8	chr2:74376000-74390400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr2:74376000-74391800	Weak transcription	Colonic Mucosa	Colon
10	chr2:74376000-74405000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr2:74376200-74384200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:74376200-74384200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:74376200-74384400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr2:74376200-74384800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:74376200-74386000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:74376200-74386000	Weak transcription	Fetal Heart	heart
17	chr2:74376200-74395200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr2:74376400-74384000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:74376400-74400600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:74376800-74386000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr2:74376800-74386200	Weak transcription	Pancreas	Pancrea
22	chr2:74376800-74391200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr2:74376800-74395400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:74376800-74397200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr2:74377000-74386200	Weak transcription	Fetal Brain Male	brain
26	chr2:74377200-74400000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr2:74377400-74400400	Strong transcription	Fetal Thymus	thymus
28	chr2:74377600-74392000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:74377600-74399200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr2:74377600-74399600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr2:74377600-74399600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:74377600-74399600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr2:74377600-74399800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr2:74377800-74384800	Strong transcription	HSMM	muscle
35	chr2:74377800-74387400	Strong transcription	NH-A	brain
36	chr2:74377800-74392000	Strong transcription	Primary monocytes fromperipheralblood	blood
37	chr2:74377800-74392000	Strong transcription	Dnd41	blood
38	chr2:74377800-74399200	Strong transcription	Primary B cells from peripheral blood	blood
39	chr2:74377800-74399400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr2:74377800-74399800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:74377800-74399800	Strong transcription	Duodenum Mucosa	Duodenum
42	chr2:74377800-74399800	Strong transcription	Placenta	Placenta
43	chr2:74377800-74400000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr2:74377800-74400200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr2:74377800-74400200	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr2:74377800-74400400	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr2:74377800-74400400	Strong transcription	A549	lung
48	chr2:74378000-74391800	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr2:74378000-74392000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr2:74378000-74399200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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