Variant report

Variant	rs10865279
Chromosome Location	chr2:54324701-54324702
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:54318413..54321728-chr2:54322663..54325829,3	K562	blood:
2	chr2:54324274..54325864-chr2:54340786..54342893,2	K562	blood:
3	chr2:54320228..54322780-chr2:54323373..54326100,2	K562	blood:

Variant related genes	Relation type
ENSG00000170634	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10207537	0.96[ASN][1000 genomes]
rs1058320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1075265	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs10865277	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10865278	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11125520	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11683654	0.82[YRI][hapmap]
rs11695734	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11887549	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11888384	0.85[ASN][1000 genomes]
rs11896781	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1215150	0.87[CHB][hapmap]
rs1363062	0.94[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs1421622	0.81[ASN][1000 genomes]
rs1559037	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1727522	0.87[CHB][hapmap]
rs1833497	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1833498	0.88[ASN][1000 genomes]
rs1862121	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1862122	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1877906	0.82[ASN][1000 genomes]
rs2018747	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2042143	0.84[ASN][1000 genomes]
rs2048749	0.83[ASN][1000 genomes]
rs2112124	0.81[ASN][1000 genomes]
rs2287642	0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2357954	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34769118	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41385746	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4671178	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4671190	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4671860	0.80[ASN][1000 genomes]
rs4671872	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs56001939	0.84[AMR][1000 genomes]
rs62137965	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62137973	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6545384	0.87[ASN][1000 genomes]
rs6545388	0.94[CHB][hapmap];0.82[CHD][hapmap]
rs6741891	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7558126	0.84[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7560947	0.87[ASN][1000 genomes]
rs7562055	0.84[ASN][1000 genomes]
rs7566894	0.94[CHB][hapmap];0.90[JPT][hapmap]
rs7569743	0.82[ASN][1000 genomes]
rs7573491	0.85[ASN][1000 genomes]
rs7574477	0.87[CHB][hapmap]
rs7590846	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7591194	0.87[ASN][1000 genomes]
rs7600141	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7604357	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7607066	0.87[ASN][1000 genomes]
rs843675	0.81[CHB][hapmap]
rs843677	0.87[CHB][hapmap]
rs888635	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs918357	0.94[CHB][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.89[ASN][1000 genomes]
rs929734	0.94[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs959285	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs959286	0.92[CEU][hapmap];0.88[CHB][hapmap];0.90[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9808326	0.84[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	nsv1001246	chr2:54195654-54434832	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
2	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
8	nsv431069	chr2:54260132-54434049	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
9	nsv1010175	chr2:54292951-54343466	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	esv1851003	chr2:54324701-54372931	Genic enhancers Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10865279	PSME4	cis	cerebellum	SCAN
rs10865279	MTIF2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54280800-54331000	Weak transcription	Aorta	Aorta
2	chr2:54291200-54342000	Weak transcription	Stomach Smooth Muscle	stomach
3	chr2:54318200-54330800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr2:54318200-54331000	Weak transcription	Brain Anterior Caudate	brain
5	chr2:54320400-54331000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr2:54321400-54327400	Weak transcription	Fetal Thymus	thymus
7	chr2:54321600-54327000	Weak transcription	Primary T cells from cord blood	blood
8	chr2:54321800-54326800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr2:54321800-54326800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:54321800-54327000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:54321800-54330800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr2:54321800-54331000	Weak transcription	Primary T helper cells PMA-I stimulated	--
13	chr2:54324000-54324800	Enhancers	HepG2	liver
14	chr2:54324000-54333400	Enhancers	Primary B cells from cord blood	blood
15	chr2:54324000-54334400	Enhancers	Primary B cells from peripheral blood	blood
16	chr2:54324200-54325000	Enhancers	GM12878-XiMat	blood
17	chr2:54324600-54325000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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