Variant report

Variant	rs7626725
Chromosome Location	chr3:150117235-150117236
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:150105059..150107937-chr3:150115799..150117722,2	K562	blood:
2	chr3:150116751..150119532-chr3:150121582..150125856,6	K562	blood:
3	chr3:150106597..150108480-chr3:150117150..150119667,2	K562	blood:
4	chr3:150108811..150111187-chr3:150116548..150119343,3	MCF-7	breast:
5	chr3:150111999..150114822-chr3:150116151..150119153,3	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10513374	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10935800	0.88[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11711035	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11719977	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12638309	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12639090	0.82[CHD][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs13080841	0.82[ASN][1000 genomes]
rs13080858	0.82[ASN][1000 genomes]
rs13082720	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099758	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13321876	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1450335	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450336	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1450344	0.83[ASW][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];0.91[JPT][hapmap];0.83[YRI][hapmap];0.92[ASN][1000 genomes]
rs16862651	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1868672	0.83[ASW][hapmap];0.94[CHB][hapmap];0.93[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.92[MKK][hapmap];0.92[YRI][hapmap];0.96[ASN][1000 genomes]
rs1868673	0.93[CHD][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs2167177	0.99[ASN][1000 genomes]
rs28514580	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2868425	0.91[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs4423794	0.91[JPT][hapmap]
rs4681205	0.82[JPT][hapmap]
rs4681206	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4681615	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4681618	0.89[CEU][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4681619	0.99[ASN][1000 genomes]
rs67319423	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6762432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770424	0.83[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.90[MKK][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs6792734	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6792759	0.83[ASW][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];0.96[MKK][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6795124	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6810143	0.83[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.96[ASN][1000 genomes]
rs7427177	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651353	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7651989	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289810	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9784281	0.99[ASN][1000 genomes]
rs9784335	0.89[CEU][hapmap];0.86[CHB][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9813752	0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs9826729	0.89[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9846873	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865031	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9882777	0.89[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[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	nsv829755	chr3:149992023-150156001	Enhancers Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	esv1828464	chr3:150096071-150149868	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv877645	chr3:150103135-150212698	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7626725	TSC22D2	cis	cerebellum	SCAN
rs7626725	AADACL2	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150090200-150124600	Weak transcription	Aorta	Aorta
2	chr3:150102800-150118200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:150109200-150124400	Weak transcription	HSMM	muscle
4	chr3:150109200-150124600	Weak transcription	NHLF	lung
5	chr3:150109600-150121200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr3:150114600-150118600	Weak transcription	Fetal Intestine Large	intestine
7	chr3:150114600-150118800	Weak transcription	Fetal Intestine Small	intestine
8	chr3:150115400-150123600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:150116800-150117400	Enhancers	H1 Cell Line	embryonic stem cell
10	chr3:150117000-150117400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr3:150117000-150117400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr3:150117000-150117400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr3:150117000-150117400	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr3:150117000-150125000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:150117200-150118600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr3:150117200-150120600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:150117200-150125000	Weak transcription	Fetal Muscle Leg	muscle

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