Variant report

Variant	rs66842594
Chromosome Location	chr1:247169258-247169259
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:247093628..247096678-chr1:247168698..247172076,4	MCF-7	breast:
2	chr1:247162509..247164222-chr1:247168923..247171107,2	MCF-7	breast:
3	chr1:247164050..247166369-chr1:247167693..247171213,3	K562	blood:

Variant related genes	Relation type
ENSG00000153207	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10924884	1.00[ASN][1000 genomes]
rs12119510	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122833	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12129167	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12734417	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12748196	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12750902	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12754486	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1691228	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2453407	0.82[ASN][1000 genomes]
rs2642993	0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2642995	0.82[ASN][1000 genomes]
rs2818876	0.82[ASN][1000 genomes]
rs3104110	0.82[ASN][1000 genomes]
rs34254934	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34651986	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35203115	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35800042	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4384270	1.00[ASN][1000 genomes]
rs4971301	0.82[ASN][1000 genomes]
rs56260816	1.00[ASN][1000 genomes]
rs56281962	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56364134	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61550625	1.00[ASN][1000 genomes]
rs61852611	0.82[ASN][1000 genomes]
rs67880452	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71638377	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73148647	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949571	chr1:246688635-247240863	Active TSS Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	nsv1006271	chr1:246832606-247276182	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv535416	chr1:246832606-247276182	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1000602	chr1:247044627-247226568	Enhancers Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
7	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
8	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
9	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
10	nsv999879	chr1:247112207-247276918	Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
11	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
12	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
13	nsv873427	chr1:247140425-247218227	ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv549546	chr1:247145690-247205056	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv945436	chr1:247162782-247171728	Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247151200-247170800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:247151600-247170000	Weak transcription	Osteobl	bone
3	chr1:247158000-247170200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:247159600-247170000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr1:247163000-247169800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr1:247163400-247170000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr1:247163400-247170000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:247163400-247170000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:247163400-247170400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr1:247163600-247170400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr1:247165600-247169600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:247166400-247170400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:247167000-247170000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr1:247168200-247170000	ZNF genes & repeats	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:247168400-247170200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:247168600-247169400	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:247168600-247170000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:247168800-247170000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:247169000-247170000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr1:247169000-247170000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr1:247169000-247170000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr1:247169000-247170000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr1:247169000-247170000	Weak transcription	Fetal Brain Female	brain
24	chr1:247169000-247170200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
25	chr1:247169000-247170400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr1:247169000-247170400	Weak transcription	Fetal Intestine Small	intestine
27	chr1:247169200-247169400	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr1:247169200-247169800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr1:247169200-247169800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:247169200-247169800	Weak transcription	Dnd41	blood
31	chr1:247169200-247169800	Weak transcription	K562	blood
32	chr1:247169200-247170200	Weak transcription	Cortex derived primary cultured neurospheres	brain

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