Variant report

Variant	rs12047494
Chromosome Location	chr1:153446797-153446798
allele	C/T
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:153445167..153447773-chr1:153461159..153464090,2	MCF-7	breast:
2	chr1:153334753..153336863-chr1:153445045..153447024,2	MCF-7	breast:
3	chr1:153327328..153331635-chr1:153443588..153448842,6	MCF-7	breast:
4	chr1:153444815..153448277-chr1:153449752..153453118,4	MCF-7	breast:
5	chr1:153330240..153331994-chr1:153445549..153448141,3	MCF-7	breast:
6	chr1:153431733..153433545-chr1:153445697..153448448,3	MCF-7	breast:
7	chr1:153443878..153448578-chr1:153449187..153452566,7	MCF-7	breast:
8	chr1:153334839..153336522-chr1:153445191..153447755,2	MCF-7	breast:
9	chr1:153441342..153443542-chr1:153445655..153447954,2	MCF-7	breast:
10	chr1:153436847..153439085-chr1:153446138..153447980,2	MCF-7	breast:
11	chr1:153445670..153449598-chr1:153450178..153453743,4	K562	blood:
12	chr1:153443002..153445359-chr1:153445547..153447150,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143556	Chromatin interaction
ENSG00000163220	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10888560	0.80[CHB][hapmap]
rs11205297	0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12021612	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12022550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12024114	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12025638	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12036701	0.80[CHB][hapmap]
rs12043280	0.89[JPT][hapmap];0.84[YRI][hapmap]
rs12043556	0.82[CHB][hapmap];0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs12044034	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12045252	0.83[AFR][1000 genomes]
rs12047203	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12217109	0.89[CHB][hapmap];0.89[JPT][hapmap];0.94[YRI][hapmap];0.84[AFR][1000 genomes]
rs16835308	0.80[CHB][hapmap]
rs16835332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16835339	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2339695	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28696717	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2986209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3006414	0.80[CHB][hapmap]
rs3006423	0.80[CHB][hapmap]
rs3014814	0.80[CHB][hapmap]
rs3014818	0.80[CHB][hapmap]
rs3014822	0.80[CHB][hapmap]
rs3014823	0.80[CHB][hapmap]
rs3014848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs41265152	0.86[AFR][1000 genomes]
rs4845348	0.80[CHB][hapmap]
rs55703007	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56009204	0.90[ASN][1000 genomes]
rs72708746	0.83[AFR][1000 genomes]
rs72708789	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv533877	chr1:152923645-153468131	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
5	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
6	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153441000-153447400	Weak transcription	Fetal Heart	heart
2	chr1:153444000-153447000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:153446400-153448000	Enhancers	Hela-S3	cervix
4	chr1:153446400-153448200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr1:153446400-153448600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr1:153446600-153447200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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