Variant report

Variant	rs2034647
Chromosome Location	chr2:173947513-173947514
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:173938088..173944133-chr2:173944779..173953152,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000091436	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10180382	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10930577	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs11681384	0.89[ASN][1000 genomes]
rs11692252	0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs1545516	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17760899	0.92[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2044515	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2358084	0.83[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs3754745	0.92[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap]
rs3754748	0.81[CEU][hapmap];0.83[CHB][hapmap];0.83[CHD][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs3769207	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4972530	0.84[EUR][1000 genomes]
rs6718374	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6727541	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6733082	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6735275	0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap]
rs6746656	0.91[CHB][hapmap]
rs6758859	0.89[CEU][hapmap];0.90[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6759787	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs73021619	0.80[AMR][1000 genomes]
rs7558132	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7558553	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7604338	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7608532	0.83[CHB][hapmap];0.88[JPT][hapmap];0.91[ASN][1000 genomes]
rs9636294	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs989531	0.81[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.88[JPT][hapmap];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs989532	0.91[ASN][1000 genomes]
rs990416	0.89[ASN][1000 genomes]
rs990417	0.89[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	nsv1011724	chr2:173916482-174231908	Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv834460	chr2:173919464-174085288	Strong transcription Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2034647	METTL8	cis	parietal	SCAN
rs2034647	SCRN3	cis	parietal	SCAN
rs2034647	ZAK	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:173941600-173955200	Weak transcription	Lung	lung
2	chr2:173941600-173955200	Weak transcription	Pancreas	Pancrea
3	chr2:173941600-173969600	Weak transcription	Spleen	Spleen
4	chr2:173941800-173955200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr2:173941800-173955200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr2:173942000-173951400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr2:173942000-173953000	Weak transcription	Stomach Mucosa	stomach
8	chr2:173942000-173955200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr2:173942000-173955400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:173942000-173956000	Weak transcription	Fetal Thymus	thymus
11	chr2:173942600-173956400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr2:173942800-173954800	Weak transcription	Monocytes-CD14+_RO01746	blood
13	chr2:173942800-173955800	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:173942800-173964600	Weak transcription	HUVEC	blood vessel
15	chr2:173942800-173971400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:173943000-173971200	Weak transcription	HSMMtube	muscle
17	chr2:173943200-173955000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:173943400-173951200	Weak transcription	Aorta	Aorta
19	chr2:173943400-173955200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr2:173943400-173955200	Weak transcription	Dnd41	blood
21	chr2:173943400-173974200	Weak transcription	Fetal Intestine Large	intestine
22	chr2:173943800-173956000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr2:173944000-173948600	Weak transcription	Adipose Nuclei	Adipose
24	chr2:173944000-173948600	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr2:173944000-173951200	Weak transcription	Fetal Lung	lung
26	chr2:173944800-173951200	Weak transcription	Fetal Stomach	stomach
27	chr2:173945000-173947600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
28	chr2:173945400-173947600	Genic enhancers	A549	lung
29	chr2:173945400-173947800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr2:173945400-173948400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr2:173945400-173991200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr2:173945600-173947800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr2:173945600-173949400	Weak transcription	NHLF	lung
34	chr2:173945600-173951200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr2:173945600-173951200	Weak transcription	Hela-S3	cervix
36	chr2:173945800-173947800	Weak transcription	Osteobl	bone
37	chr2:173945800-173951200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:173946000-173947600	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:173946000-173947600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:173946000-173947800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr2:173946200-173947600	Strong transcription	Fetal Muscle Leg	muscle
42	chr2:173946200-173948400	Weak transcription	NHDF-Ad	bronchial
43	chr2:173946200-173951200	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr2:173946600-173947600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:173946600-173947600	Enhancers	Psoas Muscle	Psoas
46	chr2:173946600-173947800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:173946800-173947600	Strong transcription	Fetal Intestine Small	intestine
48	chr2:173946800-173947600	Strong transcription	HMEC	breast
49	chr2:173946800-173947800	Enhancers	Fetal Heart	heart
50	chr2:173946800-173951800	Weak transcription	HepG2	liver

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