Variant report

Variant	rs255691
Chromosome Location	chr5:127683212-127683213
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11955288	0.86[JPT][hapmap]
rs13189118	0.86[JPT][hapmap]
rs151987	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]
rs153995	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs171527	0.94[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17676538	0.86[JPT][hapmap]
rs2291628	0.86[JPT][hapmap]
rs2307110	0.86[JPT][hapmap]
rs255690	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs26024	0.88[CHD][hapmap];0.85[ASN][1000 genomes]
rs26378	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs27754	0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs28114	0.90[CHB][hapmap];0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs32217	0.94[CHD][hapmap];0.87[ASN][1000 genomes]
rs32223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs32238	0.94[CHD][hapmap];0.97[LWK][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs331069	0.94[CHD][hapmap]
rs331071	0.89[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes]
rs331073	0.82[EUR][1000 genomes]
rs331094	0.94[CHD][hapmap]
rs331096	0.94[CEU][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs39941	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs414540	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs42281	0.83[ASN][1000 genomes]
rs458882	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs463035	0.83[ASN][1000 genomes]
rs467928	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs469070	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs469722	1.00[CHB][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs586115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs612993	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[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
rs255691	GRAMD3	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127638200-127685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:127657400-127685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr5:127658000-127683600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr5:127659200-127693600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr5:127659200-127693800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr5:127660600-127683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:127660600-127687000	Weak transcription	Fetal Brain Female	brain
8	chr5:127661200-127683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:127661200-127693000	Weak transcription	NHLF	lung
10	chr5:127661200-127693600	Strong transcription	Placenta	Placenta
11	chr5:127661800-127683600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr5:127672000-127746000	Weak transcription	NHDF-Ad	bronchial
13	chr5:127673200-127683800	Strong transcription	Fetal Stomach	stomach
14	chr5:127673800-127706400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr5:127674800-127684600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr5:127675600-127742200	Weak transcription	Fetal Intestine Small	intestine
17	chr5:127676600-127686800	Strong transcription	HUES64 Cell Line	embryonic stem cell
18	chr5:127676800-127683800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:127677600-127694800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr5:127677800-127711400	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr5:127678200-127686200	Weak transcription	NH-A	brain
22	chr5:127678600-127701000	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr5:127679200-127684600	Weak transcription	A549	lung
24	chr5:127679200-127704200	Weak transcription	Fetal Intestine Large	intestine
25	chr5:127679200-127731200	Weak transcription	Right Ventricle	heart
26	chr5:127679800-127704400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr5:127680000-127683400	Strong transcription	Primary monocytes fromperipheralblood	blood
28	chr5:127680800-127683400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr5:127681200-127685200	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr5:127681200-127689800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:127681400-127684600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr5:127681400-127684600	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr5:127681400-127684600	Weak transcription	HMEC	breast
34	chr5:127681400-127684600	Weak transcription	NHEK	skin
35	chr5:127681400-127684800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr5:127681400-127685000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr5:127681400-127685600	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:127681400-127694200	Weak transcription	Fetal Lung	lung
39	chr5:127681400-127704400	Weak transcription	Ovary	ovary
40	chr5:127681400-127706600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr5:127681600-127684400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr5:127681600-127684600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr5:127681600-127684600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr5:127681600-127684600	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr5:127681600-127685000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr5:127681600-127685000	Weak transcription	Fetal Kidney	kidney
47	chr5:127681600-127690200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:127681600-127704200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr5:127681600-127714400	Weak transcription	HUVEC	blood vessel
50	chr5:127682600-127683400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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