Variant report

Variant	rs12049168
Chromosome Location	chr1:212663815-212663816
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212662987..212664917-chr1:212706060..212707945,2	K562	blood:
2	chr1:212661275..212664884-chr1:212673911..212677045,3	K562	blood:
3	chr1:212663791..212666125-chr1:212687800..212689535,2	K562	blood:
4	chr1:212648507..212667078-chr1:212779147..212787651,52	K562	blood:
5	chr1:212663187..212667039-chr1:212686323..212689300,3	K562	blood:
6	chr1:212663370..212665864-chr1:212666315..212667949,2	K562	blood:
7	chr1:212663057..212665371-chr1:212783064..212784989,2	MCF-7	breast:
8	chr1:212645024..212669819-chr1:212778382..212791615,68	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264590	Chromatin interaction
ENSG00000162772	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10863970	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10863971	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863972	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10863975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10863978	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs11119949	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119950	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119951	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119953	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11119956	0.81[ASN][1000 genomes]
rs12030310	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12039386	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046220	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12143427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12410743	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12568048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12569340	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1807387	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs1965301	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4347269	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4951602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4951606	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4951607	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649983	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs72649985	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72649987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72649988	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649989	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72649990	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72649991	0.81[ASN][1000 genomes]
rs750227	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs750228	0.89[ASN][1000 genomes]
rs8179354	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv1013110	chr1:212555764-212948092	Flanking Active TSS Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
4	nsv535287	chr1:212555764-212948092	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	81 gene(s)	inside rSNPs	diseases
5	nsv873159	chr1:212610755-212669475	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv873160	chr1:212610755-212675482	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv873161	chr1:212610755-212683565	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv873162	chr1:212610755-212716033	Weak transcription Bivalent Enhancer Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv527863	chr1:212617423-212700618	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv873163	chr1:212629935-212669475	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	esv2757770	chr1:212648143-212843103	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases
12	esv2758996	chr1:212648143-212843103	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	77 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212650600-212667800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr1:212655000-212665800	Enhancers	Placenta	Placenta
3	chr1:212657200-212664800	Weak transcription	Spleen	Spleen
4	chr1:212660000-212664200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:212661200-212665800	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr1:212661400-212664000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:212661400-212664200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:212661400-212664200	Enhancers	Brain Substantia Nigra	brain
9	chr1:212661400-212664600	Enhancers	Brain Hippocampus Middle	brain
10	chr1:212661400-212664600	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:212661600-212664000	Enhancers	Brain Anterior Caudate	brain
12	chr1:212661600-212664200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr1:212661600-212664400	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:212662000-212664600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr1:212662600-212664800	Weak transcription	GM12878-XiMat	blood
16	chr1:212662600-212671200	Weak transcription	Left Ventricle	heart
17	chr1:212662800-212667000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr1:212662800-212671800	Weak transcription	Lung	lung
19	chr1:212663000-212664200	Weak transcription	Adipose Nuclei	Adipose
20	chr1:212663000-212664400	Weak transcription	Fetal Thymus	thymus
21	chr1:212663000-212664800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:212663000-212667000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:212663000-212671400	Weak transcription	Right Atrium	heart
24	chr1:212663200-212678400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr1:212663400-212671600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr1:212663800-212664200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr1:212663800-212664800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links