Variant report

Variant	rs16861406
Chromosome Location	chr2:174097106-174097107
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10169914	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs1345008	1.00[CEU][hapmap]
rs16861417	1.00[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.92[MEX][hapmap];0.90[TSI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2119123	0.86[CHB][hapmap];0.82[CHD][hapmap];0.84[ASN][1000 genomes]
rs2119124	0.82[JPT][hapmap]
rs3739103	0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs3754737	0.95[CHB][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3754738	0.87[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3769150	0.87[CHB][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3769151	0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[LWK][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3769152	0.86[CHB][hapmap];0.84[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs3769154	0.91[CHB][hapmap];0.86[CHD][hapmap];0.89[JPT][hapmap];0.91[ASN][1000 genomes]
rs3820831	1.00[ASW][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.90[TSI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3820832	0.87[CHB][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs41268713	0.96[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4972538	0.91[CHB][hapmap];0.82[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs72625241	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs72625242	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:174058000-174112800	Weak transcription	Spleen	Spleen
2	chr2:174061200-174097600	Weak transcription	Lung	lung
3	chr2:174063600-174097600	Weak transcription	HSMM	muscle
4	chr2:174064200-174097600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr2:174069400-174097600	Weak transcription	Primary B cells from cord blood	blood
6	chr2:174075400-174097600	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr2:174078800-174097800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr2:174082200-174097400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:174083400-174100600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr2:174083400-174136400	Weak transcription	Esophagus	oesophagus
11	chr2:174083600-174103400	Weak transcription	NHLF	lung
12	chr2:174083800-174097600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:174083800-174097600	Weak transcription	NHDF-Ad	bronchial
14	chr2:174083800-174119200	Weak transcription	HMEC	breast
15	chr2:174084600-174097600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr2:174086200-174101600	Weak transcription	Ovary	ovary
17	chr2:174086400-174098400	Weak transcription	GM12878-XiMat	blood
18	chr2:174088400-174097600	Weak transcription	Osteobl	bone
19	chr2:174089400-174097400	Weak transcription	NHEK	skin
20	chr2:174089600-174103000	Weak transcription	K562	blood
21	chr2:174092200-174109400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr2:174092400-174100600	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr2:174092400-174100600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:174092400-174101200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr2:174092800-174101200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr2:174092800-174109200	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr2:174093000-174098400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:174093000-174101200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr2:174093000-174102600	Weak transcription	Fetal Lung	lung
30	chr2:174093800-174106800	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr2:174094200-174097600	Enhancers	Fetal Thymus	thymus
32	chr2:174094200-174100800	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr2:174094400-174097800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr2:174094600-174097600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:174094800-174114600	Weak transcription	HUVEC	blood vessel
36	chr2:174095200-174097200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr2:174095200-174098600	Enhancers	Thymus	Thymus
38	chr2:174095800-174097800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr2:174095800-174098600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:174095800-174102800	Strong transcription	Fetal Stomach	stomach
41	chr2:174096000-174128800	Weak transcription	Sigmoid Colon	Sigmoid Colon
42	chr2:174096200-174098200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr2:174096200-174100200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr2:174096200-174100800	Weak transcription	Primary B cells from peripheral blood	blood
45	chr2:174096200-174102400	Weak transcription	Stomach Mucosa	stomach
46	chr2:174096200-174118200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr2:174096400-174097600	Weak transcription	Colon Smooth Muscle	Colon
48	chr2:174096400-174098600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:174096400-174098800	Strong transcription	Dnd41	blood
50	chr2:174096400-174100200	Weak transcription	Brain Germinal Matrix	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links