Variant report

Variant	rs1408828
Chromosome Location	chr1:156352351-156352352
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:7)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:156351935..156356814-chr1:156357116..156361846,4	MCF-7	breast:
2	chr1:156335306..156343282-chr1:156347773..156352892,8	MCF-7	breast:
3	chr1:156326525..156327327-chr1:156352210..156353356,4	MCF-7	breast:
4	chr1:156352086..156353955-chr1:156559602..156561558,2	MCF-7	breast:
5	chr1:156352334..156353343-chr1:156414003..156414885,7	MCF-7	breast:
6	chr1:156341941..156343974-chr1:156352114..156354913,2	K562	blood:
7	chr1:156351422..156354459-chr1:156356280..156359051,3	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C1orf182-1	chr1:156352104-156352660	NONHSAT006846

No data

No data

Variant related genes	Relation type
ENSG00000163468	Chromatin interaction
ENSG00000237390	Chromatin interaction
ENSG00000132677	Chromatin interaction
ENSG00000163382	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs3790462	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs872120	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs954916	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases
2	nsv1011302	chr1:156081561-156532624	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	380 gene(s)	inside rSNPs	diseases
3	nsv915822	chr1:156226286-156651655	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	367 gene(s)	inside rSNPs	diseases
4	nsv872471	chr1:156287360-156356480	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
5	nsv470742	chr1:156335111-156354367	Genic enhancers Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	esv1793632	chr1:156338992-156366178	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
7	nsv1005335	chr1:156347358-156905648	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	395 gene(s)	inside rSNPs	diseases
8	nsv1004910	chr1:156347358-157258223	Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	430 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:156339600-156358000	Weak transcription	Right Atrium	heart
2	chr1:156346000-156355000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr1:156346200-156354800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr1:156347400-156353800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr1:156347600-156353800	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:156348200-156354200	Weak transcription	Ovary	ovary
7	chr1:156349800-156352400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:156349800-156355000	Weak transcription	HSMM	muscle
9	chr1:156349800-156355600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:156349800-156355600	Weak transcription	A549	lung
11	chr1:156349800-156356000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:156351000-156352800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:156351000-156353000	Strong transcription	Fetal Intestine Large	intestine
14	chr1:156351200-156355600	Strong transcription	Fetal Intestine Small	intestine
15	chr1:156351400-156353200	Genic enhancers	HepG2	liver
16	chr1:156352200-156353000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin

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dbSNP/dbVar ID: rs12345 /nsv7879
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