Variant report

Variant	rs1233665
Chromosome Location	chr6:28178512-28178513
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28167517..28171168-chr6:28177888..28180588,3	K562	blood:
2	chr6:28122889..28124668-chr6:28176710..28180566,3	K562	blood:
3	chr6:28177601..28182191-chr6:28315411..28319291,5	K562	blood:
4	chr6:28103936..28106419-chr6:28177015..28179334,3	MCF-7	breast:
5	chr6:28104315..28106178-chr6:28177345..28180593,3	MCF-7	breast:
6	chr6:28108322..28111152-chr6:28178112..28181694,4	K562	blood:
7	chr6:28178232..28180361-chr6:28366158..28368738,2	K562	blood:
8	chr6:28177473..28179132-chr6:28218627..28221349,2	MCF-7	breast:
9	chr6:28178129..28180295-chr6:28233395..28236371,2	K562	blood:
10	chr6:28103775..28107091-chr6:28177064..28180460,3	K562	blood:
11	chr6:28151155..28153263-chr6:28178363..28180275,2	K562	blood:
12	chr6:28178359..28182415-chr6:28302345..28306363,5	K562	blood:
13	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
14	chr6:27864015..27866427-chr6:28176005..28180203,3	K562	blood:
15	chr6:28176585..28178668-chr6:28184409..28186651,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197062	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000187626	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10484404	0.90[CEU][hapmap]
rs1062169	0.94[GIH][hapmap];0.83[TSI][hapmap]
rs1150697	0.81[CEU][hapmap]
rs1150698	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150699	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1150704	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1150714	0.80[CEU][hapmap]
rs11752073	0.90[CEU][hapmap]
rs11758148	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs1233664	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233666	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1474589	0.80[CEU][hapmap]
rs16893552	0.80[CEU][hapmap]
rs16893817	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs16893937	0.80[CEU][hapmap]
rs16901846	0.80[CEU][hapmap]
rs1736890	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1736894	0.94[ASW][hapmap];0.91[CEU][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1778469	0.84[JPT][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1778477	0.91[GIH][hapmap]
rs1890809	0.90[CEU][hapmap]
rs2232422	0.80[CEU][hapmap]
rs2281043	0.80[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs2622315	0.90[CEU][hapmap]
rs3800325	0.80[CEU][hapmap]
rs4141691	0.80[CEU][hapmap]
rs6456811	0.80[CEU][hapmap];0.91[GIH][hapmap];0.83[TSI][hapmap]
rs6917759	0.90[CEU][hapmap]
rs6923170	0.80[CEU][hapmap]
rs6929559	0.90[CEU][hapmap]
rs73740584	0.96[EUR][1000 genomes]
rs73740587	0.90[EUR][1000 genomes]
rs7744788	0.80[CEU][hapmap]
rs7769054	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs993619	1.00[CEU][hapmap];0.81[GIH][hapmap];0.88[TSI][hapmap];0.88[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	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883515	chr6:28156476-28181675	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1233665		cis	Lymphoblastoid	GTEx
rs1233665	ZNF192P1	cis	Adipose Subcutaneous	GTEx
rs1233665	AL022393.7	cis	Thyroid	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28177800-28179200	Enhancers	K562	blood
2	chr6:28178200-28179400	Weak transcription	HMEC	breast
3	chr6:28178200-28179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:28178200-28179600	Weak transcription	NHEK	skin
5	chr6:28178400-28180000	Weak transcription	HSMMtube	muscle

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