Variant report

Variant	rs151987
Chromosome Location	chr5:127686378-127686379
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	chr5:127548617..127549644-chr5:127686173..127687070,3	MCF-7	breast:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11955288	0.86[JPT][hapmap]
rs13189118	0.86[JPT][hapmap]
rs153995	0.85[ASN][1000 genomes]
rs171527	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs17676538	0.86[JPT][hapmap]
rs2291628	0.86[JPT][hapmap]
rs2307110	0.86[JPT][hapmap]
rs255690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs255691	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs26024	0.92[CEU][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs26378	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs27457	0.81[ASN][1000 genomes]
rs27754	0.83[CHD][hapmap]
rs28114	0.90[CHB][hapmap];0.94[CHD][hapmap];0.89[ASN][1000 genomes]
rs32217	0.96[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs32223	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs32238	0.93[ASW][hapmap];0.96[CEU][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.88[AFR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs331069	0.94[CHD][hapmap]
rs331071	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[JPT][hapmap]
rs331094	0.94[CHD][hapmap]
rs331096	0.94[CHD][hapmap]
rs331099	0.86[EUR][1000 genomes]
rs39941	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs414540	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs42281	0.96[CEU][hapmap];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs458882	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs463035	0.82[ASN][1000 genomes]
rs467928	0.90[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs469070	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs469722	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs586115	1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs612993	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599697	chr5:127563563-127731210	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv830483	chr5:127595570-127705124	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
3	nsv531991	chr5:127624564-127966085	Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs151987	GRAMD3	cis	parietal	SCAN

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127659200-127693600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr5:127659200-127693800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:127660600-127687000	Weak transcription	Fetal Brain Female	brain
4	chr5:127661200-127693000	Weak transcription	NHLF	lung
5	chr5:127661200-127693600	Strong transcription	Placenta	Placenta
6	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
7	chr5:127673800-127706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr5:127675600-127742200	Weak transcription	Fetal Intestine Small	intestine
9	chr5:127676600-127686800	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr5:127677600-127694800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr5:127677800-127711400	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr5:127678600-127701000	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr5:127679200-127704200	Weak transcription	Fetal Intestine Large	intestine
14	chr5:127679200-127731200	Weak transcription	Right Ventricle	heart
15	chr5:127679800-127704400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr5:127681200-127689800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr5:127681400-127694200	Weak transcription	Fetal Lung	lung
18	chr5:127681400-127704400	Weak transcription	Ovary	ovary
19	chr5:127681400-127706600	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr5:127681600-127690200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr5:127681600-127704200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr5:127681600-127714400	Weak transcription	HUVEC	blood vessel
23	chr5:127682800-127686400	Weak transcription	Left Ventricle	heart
24	chr5:127682800-127688800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr5:127683800-127692000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
26	chr5:127684400-127687800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:127684600-127686600	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr5:127684600-127686800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr5:127684600-127687000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr5:127684800-127689000	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:127685000-127686600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr5:127685000-127687600	Strong transcription	Fetal Stomach	stomach
33	chr5:127685000-127688200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr5:127685000-127691200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr5:127685200-127686600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr5:127685200-127689200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr5:127685400-127686400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr5:127685400-127686800	Strong transcription	Fetal Muscle Leg	muscle
39	chr5:127685400-127690400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr5:127685400-127725000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:127685600-127686400	Weak transcription	Placenta Amnion	Placenta Amnion
42	chr5:127685600-127687600	Strong transcription	Fetal Muscle Trunk	muscle
43	chr5:127685600-127691800	Weak transcription	NHEK	skin
44	chr5:127685600-127704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr5:127685800-127686600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr5:127685800-127687000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr5:127685800-127694000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr5:127685800-127702000	Weak transcription	HMEC	breast
49	chr5:127685800-127712400	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:127686000-127688200	Weak transcription	Fetal Kidney	kidney

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