Variant report

Variant	rs6868222
Chromosome Location	chr5:57154446-57154447
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:57153108..57154848-chr5:57753681..57756204,2	MCF-7	breast:
2	chr5:57076424..57079221-chr5:57153690..57156496,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145632	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs12519846	0.89[EUR][1000 genomes]
rs12654378	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16887464	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16887469	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1821211	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1835873	0.86[ASN][1000 genomes]
rs1835875	0.85[ASN][1000 genomes]
rs2408855	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34152283	0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34397458	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34711481	0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35483666	0.91[EUR][1000 genomes]
rs4432842	0.80[ASW][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.83[YRI][hapmap]
rs4562008	0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs6892809	0.89[EUR][1000 genomes]
rs7701201	0.83[ASN][1000 genomes]
rs7716711	0.91[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs7717208	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7721249	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7722730	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs854034	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525330	chr5:56931673-57320343	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	esv2756302	chr5:56978143-57180143	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv830310	chr5:56989346-57176006	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2763454	chr5:57006531-57161140	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6868222	IL6ST	cis	cerebellum	SCAN
rs6868222	GPX8	cis	parietal	SCAN
rs6868222	PLK2	cis	cerebellum	SCAN
rs6868222	DHX29	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57150600-57154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:57151200-57158200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr5:57151400-57160000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr5:57152600-57155800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr5:57153400-57154600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr5:57153800-57155400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr5:57154000-57155200	Weak transcription	NHEK	skin
8	chr5:57154000-57157200	Weak transcription	HMEC	breast
9	chr5:57154200-57155000	Enhancers	Fetal Heart	heart
10	chr5:57154400-57155000	Enhancers	Fetal Muscle Leg	muscle
11	chr5:57154400-57155000	Enhancers	Right Atrium	heart
12	chr5:57154400-57155600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr5:57154400-57155600	Enhancers	HSMM	muscle

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