Variant report

Variant	rs719008
Chromosome Location	chr12:48416052-48416053
allele	A/C
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	chr12:48357498..48359897-chr12:48415530..48417456,2	MCF-7	breast:
2	chr12:48415272..48418773-chr12:48419086..48422802,6	MCF-7	breast:
3	chr12:48212416..48215175-chr12:48415223..48418079,4	MCF-7	breast:
4	chr12:48415871..48417650-chr12:48439843..48442703,2	MCF-7	breast:
5	chr12:48407751..48410923-chr12:48414618..48417182,4	MCF-7	breast:
6	chr12:48415815..48418237-chr12:48421031..48422834,2	K562	blood:
7	chr12:48292355..48294336-chr12:48414292..48417246,2	MCF-7	breast:
8	chr12:48294511..48296971-chr12:48414193..48417151,2	MCF-7	breast:
9	chr12:48406038..48410831-chr12:48411860..48418424,9	MCF-7	breast:
10	chr12:48391315..48400584-chr12:48411914..48418489,16	MCF-7	breast:
11	chr12:48367607..48371765-chr12:48415495..48417356,3	MCF-7	breast:
12	chr12:48410357..48413530-chr12:48413703..48417962,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134291	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000139219	Chromatin interaction
ENSG00000257955	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs10082861	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs10219623	0.93[JPT][hapmap]
rs10875720	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875722	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10875724	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875725	0.90[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875730	0.91[ASN][1000 genomes]
rs10875731	0.91[ASN][1000 genomes]
rs10875732	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs10875745	0.93[JPT][hapmap]
rs10875746	0.93[JPT][hapmap]
rs10875750	0.93[JPT][hapmap]
rs10875767	0.87[JPT][hapmap]
rs10875770	0.86[JPT][hapmap]
rs10875772	0.86[JPT][hapmap]
rs11168355	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs11168357	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11168369	0.94[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168371	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs11168374	0.91[ASN][1000 genomes]
rs11168403	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs11168413	0.93[JPT][hapmap]
rs11168414	0.93[JPT][hapmap]
rs11168418	0.93[JPT][hapmap]
rs11168420	0.93[JPT][hapmap]
rs11168421	0.93[JPT][hapmap]
rs11168425	0.93[JPT][hapmap]
rs11168427	0.93[JPT][hapmap]
rs11168433	0.93[JPT][hapmap]
rs11168450	0.93[JPT][hapmap]
rs11168459	0.86[JPT][hapmap]
rs12296244	0.91[ASN][1000 genomes]
rs12297470	0.93[JPT][hapmap]
rs12304476	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12305182	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12305511	0.93[JPT][hapmap]
rs12306451	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs12310813	0.93[JPT][hapmap]
rs12310999	0.91[ASN][1000 genomes]
rs12312134	0.87[JPT][hapmap]
rs17122666	0.93[JPT][hapmap]
rs17122812	0.87[JPT][hapmap]
rs1859445	0.93[JPT][hapmap]
rs2012773	0.93[JPT][hapmap]
rs2079295	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2107638	0.93[JPT][hapmap]
rs2228500	0.93[JPT][hapmap]
rs2269933	0.93[JPT][hapmap]
rs2269935	0.93[JPT][hapmap]
rs2269936	0.95[CHB][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs28459711	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782910	0.95[CHB][hapmap];0.93[JPT][hapmap]
rs4760609	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs4760610	0.96[ASN][1000 genomes]
rs4760619	0.93[JPT][hapmap]
rs4760622	0.93[JPT][hapmap]
rs4760676	0.93[ASN][1000 genomes]
rs4760681	0.93[JPT][hapmap]
rs4760687	0.93[JPT][hapmap]
rs4760695	0.93[JPT][hapmap]
rs4760696	0.93[JPT][hapmap]
rs4760697	0.93[JPT][hapmap]
rs61918774	0.91[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap]
rs7135779	0.93[JPT][hapmap]
rs725454	0.93[JPT][hapmap]
rs7299135	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299271	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299364	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7299762	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7486424	0.93[JPT][hapmap]
rs7964359	0.88[CHB][hapmap];0.80[JPT][hapmap];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs8804	0.93[JPT][hapmap]
rs886588	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs989144	0.95[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2760677	chr12:48412410-48416967	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs719008	ZNF641	cis	Whole Blood	GTEx
rs719008	H1FNT	cis	Muscle Skeletal	GTEx
rs719008	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs719008	ZNF641	cis	Muscle Skeletal	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48415000-48416800	Enhancers	Right Atrium	heart
2	chr12:48415000-48417800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr12:48415000-48417800	Enhancers	Fetal Lung	lung
4	chr12:48415000-48417800	Enhancers	Rectal Mucosa Donor 31	rectum
5	chr12:48415000-48418000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr12:48415000-48418200	Enhancers	Fetal Intestine Large	intestine
7	chr12:48415000-48418200	Enhancers	Fetal Intestine Small	intestine
8	chr12:48415200-48416800	Enhancers	Placenta	Placenta
9	chr12:48415200-48418000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:48415200-48418200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr12:48415400-48417000	Enhancers	Right Ventricle	heart
12	chr12:48415400-48417800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr12:48415400-48417800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
14	chr12:48415400-48418000	Enhancers	Fetal Heart	heart
15	chr12:48415400-48418000	Enhancers	HepG2	liver
16	chr12:48415600-48416600	Weak transcription	Left Ventricle	heart
17	chr12:48415800-48416200	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
18	chr12:48415800-48416800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr12:48415800-48417200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:48415800-48417200	Weak transcription	Pancreas	Pancrea
21	chr12:48415800-48417400	Enhancers	Lung	lung
22	chr12:48415800-48420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:48416000-48416400	Weak transcription	Gastric	stomach
24	chr12:48416000-48416600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr12:48416000-48416600	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
26	chr12:48416000-48416600	Weak transcription	Duodenum Mucosa	Duodenum
27	chr12:48416000-48416800	Enhancers	Hela-S3	cervix
28	chr12:48416000-48417000	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr12:48416000-48417200	Weak transcription	A549	lung
30	chr12:48416000-48417800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
31	chr12:48416000-48418000	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell

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