Variant report

Variant	rs469722
Chromosome Location	chr5:127666565-127666566
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	chr5:127664970..127667943-chr5:127669467..127671261,2	K562	blood:
2	chr5:127663410..127665396-chr5:127666243..127668383,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11955288	0.86[JPT][hapmap]
rs13189118	0.86[JPT][hapmap]
rs151987	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]
rs171527	0.90[CHB][hapmap];0.88[JPT][hapmap];0.98[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];0.82[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs255691	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]
rs26024	0.92[CEU][hapmap];0.95[GIH][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs26378	0.88[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs28114	0.90[CHB][hapmap];0.84[CHD][hapmap];0.88[ASN][1000 genomes]
rs32217	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs32223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs32238	0.86[ASW][hapmap];0.96[CEU][hapmap];0.92[GIH][hapmap];0.88[LWK][hapmap];0.83[MKK][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs331071	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs331099	0.85[EUR][1000 genomes]
rs39941	0.93[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs414540	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs42281	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs458882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs463035	0.89[ASN][1000 genomes]
rs467928	0.93[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs469070	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs586115	1.00[CHB][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs612993	0.95[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
rs469722	GRAMD3	cis	parietal	SCAN

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127589000-127670200	Weak transcription	NHDF-Ad	bronchial
2	chr5:127638200-127685000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr5:127655600-127667000	Weak transcription	NHEK	skin
4	chr5:127657400-127685000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr5:127658000-127683600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr5:127659200-127693600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:127659200-127693800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:127660600-127668000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr5:127660600-127668000	Weak transcription	Hela-S3	cervix
10	chr5:127660600-127683800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:127660600-127687000	Weak transcription	Fetal Brain Female	brain
12	chr5:127661000-127667400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr5:127661000-127675800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr5:127661200-127674800	Strong transcription	Muscle Satellite Cultured Cells	--
15	chr5:127661200-127675600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr5:127661200-127683800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr5:127661200-127693000	Weak transcription	NHLF	lung
18	chr5:127661200-127693600	Strong transcription	Placenta	Placenta
19	chr5:127661400-127667200	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr5:127661800-127675000	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr5:127661800-127683600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr5:127662000-127667400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:127662000-127674400	Weak transcription	Fetal Intestine Small	intestine
24	chr5:127662000-127681400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr5:127662400-127668600	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr5:127662400-127674800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:127662400-127675800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr5:127663200-127670000	Weak transcription	HUVEC	blood vessel
29	chr5:127663200-127675400	Weak transcription	Fetal Intestine Large	intestine
30	chr5:127663600-127667800	Strong transcription	A549	lung
31	chr5:127663600-127668600	Strong transcription	Placenta Amnion	Placenta Amnion
32	chr5:127664200-127673200	Weak transcription	NH-A	brain
33	chr5:127664600-127667000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr5:127664600-127669600	Weak transcription	Left Ventricle	heart
35	chr5:127664600-127670200	Weak transcription	Ovary	ovary
36	chr5:127664600-127671400	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr5:127664600-127673200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr5:127664600-127678800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr5:127664600-127682000	Weak transcription	Duodenum Smooth Muscle	Duodenum
40	chr5:127665000-127666800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr5:127665200-127669800	Weak transcription	Right Ventricle	heart
42	chr5:127665400-127667200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr5:127665400-127669400	Strong transcription	Fetal Heart	heart
44	chr5:127665400-127674600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr5:127665400-127676600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr5:127665600-127666600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:127665600-127666600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr5:127666200-127666800	Strong transcription	Fetal Kidney	kidney
49	chr5:127666200-127667400	Strong transcription	Fetal Lung	lung
50	chr5:127666200-127667600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell

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