Variant report

Variant	rs7438356
Chromosome Location	chr4:15624770-15624771
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	chr4:15607476..15609952-chr4:15624488..15626808,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10008376	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];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10008975	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];0.92[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10214	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10939621	0.85[JPT][hapmap];0.82[YRI][hapmap]
rs11728084	0.88[EUR][1000 genomes]
rs12499412	0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500587	1.00[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs12500770	0.80[AFR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12512883	0.87[EUR][1000 genomes]
rs12644655	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12649803	0.86[JPT][hapmap]
rs12651550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13110674	0.92[EUR][1000 genomes]
rs13120905	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13129739	0.87[EUR][1000 genomes]
rs13147590	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1789	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35414597	0.88[EUR][1000 genomes]
rs4235379	0.96[CEU][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs4270584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4333182	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4453929	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4470622	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4524378	0.91[EUR][1000 genomes]
rs4557256	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4616746	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4631041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4698402	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4698404	0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698406	0.93[EUR][1000 genomes]
rs4698407	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4698409	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61021642	0.91[EUR][1000 genomes]
rs6414765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6414767	0.82[AFR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414768	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6449146	0.86[JPT][hapmap]
rs6449147	0.86[JPT][hapmap];0.80[YRI][hapmap]
rs6449153	0.96[EUR][1000 genomes]
rs6449161	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6850169	0.84[EUR][1000 genomes]
rs6850422	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.88[YRI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs759212	0.86[JPT][hapmap];0.86[YRI][hapmap]
rs7662032	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7685083	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];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7687003	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7688984	0.94[EUR][1000 genomes]
rs7696127	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7697314	0.86[JPT][hapmap]
rs9996452	0.86[JPT][hapmap]
rs9997068	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3448986	chr4:14928802-15805558	Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	esv2757923	chr4:15444617-15749520	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	esv2759227	chr4:15444617-15749520	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv428439	chr4:15556961-15749520	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv1012988	chr4:15597510-16091527	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv518830	chr4:15610771-15672200	Flanking Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv521183	chr4:15610771-15692136	Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
8	esv3376437	chr4:15613963-15626944	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv3464784	chr4:15613969-15626901	Strong transcription ZNF genes & repeats Weak transcription Enhancers Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv3464785	chr4:15613969-15626901	ZNF genes & repeats Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7438356	BST1	cis	multi-tissue	Pritchard
rs7438356	FBXL5	cis	multi-tissue	Pritchard
rs7438356	FBXL5	cis	Liver	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:15568400-15655600	Weak transcription	Gastric	stomach
2	chr4:15590600-15626400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:15600800-15653000	Weak transcription	Colonic Mucosa	Colon
4	chr4:15601000-15651600	Weak transcription	Small Intestine	intestine
5	chr4:15602000-15626000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr4:15602600-15655600	Weak transcription	Pancreas	Pancrea
7	chr4:15603800-15626800	Weak transcription	NHLF	lung
8	chr4:15605400-15625800	Weak transcription	HMEC	breast
9	chr4:15605800-15650200	Weak transcription	Stomach Mucosa	stomach
10	chr4:15606000-15633800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr4:15612800-15625200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr4:15613400-15625800	Weak transcription	NH-A	brain
13	chr4:15613400-15626200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr4:15613400-15635000	Weak transcription	HSMMtube	muscle
15	chr4:15613600-15626000	Weak transcription	Placenta	Placenta
16	chr4:15615600-15625000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr4:15617800-15627400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr4:15618600-15625800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr4:15618600-15626000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr4:15618600-15627000	Weak transcription	Right Ventricle	heart
21	chr4:15618600-15651000	Weak transcription	Spleen	Spleen
22	chr4:15620600-15624800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr4:15620800-15626800	Weak transcription	Lung	lung
24	chr4:15621000-15624800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:15621000-15624800	ZNF genes & repeats	Dnd41	blood
26	chr4:15621000-15632600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr4:15621200-15625200	ZNF genes & repeats	GM12878-XiMat	blood
28	chr4:15621600-15625800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr4:15621600-15625800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr4:15621600-15625800	Weak transcription	Osteobl	bone
31	chr4:15621600-15627000	Weak transcription	Brain Angular Gyrus	brain
32	chr4:15621800-15625600	Weak transcription	HUVEC	blood vessel
33	chr4:15621800-15625800	Weak transcription	Fetal Kidney	kidney
34	chr4:15621800-15625800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr4:15621800-15626000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
36	chr4:15621800-15626000	Weak transcription	Stomach Smooth Muscle	stomach
37	chr4:15621800-15626000	Weak transcription	NHEK	skin
38	chr4:15621800-15626200	Weak transcription	Hela-S3	cervix
39	chr4:15621800-15626400	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr4:15621800-15626800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:15621800-15626800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr4:15621800-15626800	Weak transcription	Rectal Smooth Muscle	rectum
43	chr4:15621800-15627000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr4:15621800-15627000	Weak transcription	Esophagus	oesophagus
45	chr4:15621800-15627000	Weak transcription	Psoas Muscle	Psoas
46	chr4:15622200-15624800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr4:15622200-15625400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr4:15622200-15625800	Weak transcription	Colon Smooth Muscle	Colon
49	chr4:15622200-15625800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr4:15622200-15626000	Weak transcription	Fetal Lung	lung

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