Variant report

Variant	rs3001261
Chromosome Location	chr1:212650352-212650353
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:212648977..212651974-chr1:212781395..212783104,2	MCF-7	breast:
2	chr1:212650198..212651416-chr1:212803125..212803807,3	MCF-7	breast:
3	chr1:212650231..212651131-chr1:213168597..213169449,2	K562	blood:
4	chr1:212650238..212651131-chr1:212955932..212956435,2	K562	blood:
5	chr1:212650032..212653623-chr1:212730266..212733190,4	K562	blood:
6	chr1:212645805..212648932-chr1:212650111..212654210,5	K562	blood:
7	chr1:212643908..212648932-chr1:212649184..212654651,9	K562	blood:
8	chr1:212650191..212651259-chr1:212838184..212839254,5	K562	blood:
9	chr1:212648507..212667078-chr1:212779147..212787651,52	K562	blood:
10	chr1:212650264..212651134-chr1:212782287..212782879,2	MCF-7	breast:
11	chr1:212650175..212651195-chr1:212803104..212804056,5	K562	blood:
12	chr1:212645024..212669819-chr1:212778382..212791615,68	K562	blood:
13	chr1:8928491..8931426-chr1:212648815..212650647,2	K562	blood:
14	chr1:212641496..212643517-chr1:212649175..212651881,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000264590	Chromatin interaction
ENSG00000260805	Chromatin interaction
ENSG00000162772	Chromatin interaction
ENSG00000074800	Chromatin interaction
ENSG00000237980	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11571524	1.00[AMR][1000 genomes]
rs11571533	1.00[AMR][1000 genomes]
rs11571535	1.00[AMR][1000 genomes]
rs11571558	1.00[AMR][1000 genomes]
rs12739715	1.00[ASN][1000 genomes]
rs17019266	1.00[ASN][1000 genomes]
rs17019397	1.00[ASN][1000 genomes]
rs2007776	1.00[ASN][1000 genomes]
rs35030678	1.00[ASN][1000 genomes]
rs492231	1.00[ASN][1000 genomes]
rs498564	1.00[ASN][1000 genomes]
rs56085986	1.00[ASN][1000 genomes]
rs58475088	1.00[AMR][1000 genomes]
rs593750	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs60028272	1.00[AMR][1000 genomes]
rs641053	1.00[ASN][1000 genomes]
rs648577	1.00[ASN][1000 genomes]
rs6680374	1.00[ASN][1000 genomes]
rs71646161	1.00[ASN][1000 genomes]
rs73075890	1.00[AMR][1000 genomes]
rs73075893	1.00[AMR][1000 genomes]
rs73075901	1.00[AMR][1000 genomes]
rs73077743	1.00[AMR][1000 genomes]
rs73077745	1.00[AMR][1000 genomes]
rs73077750	1.00[AMR][1000 genomes]
rs73077752	1.00[AMR][1000 genomes]
rs73077765	1.00[AMR][1000 genomes]
rs73077787	1.00[AMR][1000 genomes]
rs73077796	1.00[AMR][1000 genomes]
rs73077801	1.00[AMR][1000 genomes]
rs73079812	1.00[AMR][1000 genomes]
rs73079819	1.00[AMR][1000 genomes]
rs73079839	1.00[AMR][1000 genomes]
rs73079842	1.00[AMR][1000 genomes]
rs73088535	1.00[AMR][1000 genomes]
rs73088538	1.00[AMR][1000 genomes]
rs73088542	1.00[AMR][1000 genomes]
rs73088546	1.00[AMR][1000 genomes]
rs73090557	1.00[AMR][1000 genomes]
rs74138553	1.00[ASN][1000 genomes]
rs74138559	1.00[ASN][1000 genomes]
rs7530106	1.00[ASN][1000 genomes]
rs7549085	1.00[ASN][1000 genomes]
rs7551910	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212641000-212650400	Weak transcription	Fetal Intestine Large	intestine
2	chr1:212641600-212658200	Weak transcription	Gastric	stomach
3	chr1:212641800-212655200	Weak transcription	Right Atrium	heart
4	chr1:212643800-212652400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:212644200-212650400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr1:212645000-212652400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr1:212645200-212650400	Weak transcription	Stomach Mucosa	stomach
8	chr1:212647400-212650400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr1:212648800-212650400	Weak transcription	Brain Anterior Caudate	brain
10	chr1:212649000-212650400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:212649000-212650400	Weak transcription	Brain Angular Gyrus	brain
12	chr1:212649000-212650400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr1:212649000-212650400	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr1:212650000-212650400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr1:212650200-212650600	Enhancers	Brain Hippocampus Middle	brain
16	chr1:212650200-212651000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:212650200-212651600	Enhancers	Brain Substantia Nigra	brain
18	chr1:212650200-212651600	Enhancers	GM12878-XiMat	blood

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