Variant report

Variant	rs6819605
Chromosome Location	chr4:75145581-75145582
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	FAM48A	chr4:75145533-75145608	GM12878	blood:	n/a	n/a
2	POLR2A	chr4:75145451-75148125	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr4:75143302..75145646-chr4:75147933..75149559,2	K562	blood:
2	chr4:75024505..75027399-chr4:75144223..75145811,2	K562	blood:
3	chr4:75023332..75025369-chr4:75145514..75147366,2	MCF-7	breast:
4	chr4:75133705..75136322-chr4:75143940..75145615,2	MCF-7	breast:

Variant related genes	Relation type
MTHFD2L	TF binding region
ENSG00000269559	Chromatin interaction
ENSG00000163738	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10009707	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10010575	0.97[TSI][hapmap];0.86[EUR][1000 genomes]
rs10013212	0.90[EUR][1000 genomes]
rs10017409	0.81[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10017417	0.82[EUR][1000 genomes]
rs10018373	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs10019396	0.81[CEU][hapmap];0.91[EUR][1000 genomes]
rs10023519	0.82[CEU][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes]
rs10026687	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs10028285	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1037824	0.97[EUR][1000 genomes]
rs10433673	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10938112	0.91[EUR][1000 genomes]
rs11724468	0.90[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11737662	0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs1246575	0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs1246577	0.82[EUR][1000 genomes]
rs1246578	0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs1246579	0.80[EUR][1000 genomes]
rs1246582	0.82[EUR][1000 genomes]
rs1246584	0.82[EUR][1000 genomes]
rs1246586	0.82[EUR][1000 genomes]
rs1246587	0.82[EUR][1000 genomes]
rs1246588	0.82[EUR][1000 genomes]
rs1246590	0.80[EUR][1000 genomes]
rs1246591	0.80[CEU][hapmap];0.87[CHB][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs12500697	0.81[EUR][1000 genomes]
rs1265327	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs13116896	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13142241	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1371796	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1371797	0.88[CHB][hapmap]
rs1380561	0.85[EUR][1000 genomes]
rs1460016	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16850862	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16850883	0.93[CEU][hapmap];0.97[EUR][1000 genomes]
rs17232394	0.90[EUR][1000 genomes]
rs17829765	0.89[TSI][hapmap]
rs1964526	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2045616	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs2045617	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs2045618	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2061508	0.94[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2367555	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2367745	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28378517	0.87[EUR][1000 genomes]
rs28436705	0.89[EUR][1000 genomes]
rs28539097	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28644493	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28695994	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4371587	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4502653	0.90[EUR][1000 genomes]
rs4577545	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4694184	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs488440	0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs58813617	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62312513	0.82[EUR][1000 genomes]
rs62312515	0.85[EUR][1000 genomes]
rs62312545	0.89[EUR][1000 genomes]
rs6446983	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6446984	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446985	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6814880	0.95[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs6820992	0.95[CEU][hapmap];0.97[EUR][1000 genomes]
rs6821664	0.82[CEU][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes]
rs6835734	0.95[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs6854203	0.84[EUR][1000 genomes]
rs6854723	0.82[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs715844	0.85[EUR][1000 genomes]
rs7659389	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7663269	0.94[ASW][hapmap];0.83[CEU][hapmap];0.88[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.92[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7665105	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7670535	0.89[EUR][1000 genomes]
rs7672588	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7681137	0.88[CHB][hapmap];0.81[GIH][hapmap]
rs7681912	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7683181	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9992393	0.85[EUR][1000 genomes]
rs9997322	0.82[CEU][hapmap];0.92[TSI][hapmap];0.89[EUR][1000 genomes]
rs9997788	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525980	chr4:74731526-75382209	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1009099	chr4:75089233-75726206	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription Genic 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	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6819605	ANKRD56	cis	parietal	SCAN
rs6819605	CNOT6L	cis	parietal	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:75119800-75148800	Weak transcription	Aorta	Aorta
2	chr4:75125200-75158800	Weak transcription	Left Ventricle	heart
3	chr4:75132200-75157800	Weak transcription	Brain Hippocampus Middle	brain
4	chr4:75133800-75160000	Weak transcription	Liver	Liver
5	chr4:75134000-75173800	Weak transcription	Primary T cells from cord blood	blood
6	chr4:75134400-75148800	Weak transcription	HSMM	muscle
7	chr4:75134600-75148400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr4:75134800-75148200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr4:75134800-75148200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr4:75134800-75148800	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr4:75135000-75147600	Weak transcription	HMEC	breast
12	chr4:75139600-75147600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:75140200-75146000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr4:75141200-75147200	Strong transcription	Primary hematopoietic stem cells	blood
15	chr4:75141800-75151200	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr4:75144000-75153200	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr4:75144400-75162000	Weak transcription	Primary B cells from cord blood	blood
18	chr4:75144600-75149200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr4:75144800-75145600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr4:75144800-75145800	Weak transcription	NHEK	skin
21	chr4:75144800-75149400	Weak transcription	K562	blood

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