Variant report

Variant	rs10479871
Chromosome Location	chr7:47723480-47723481
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 56 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10224672	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10226633	0.86[AFR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10226887	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10227002	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10227130	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10234095	0.88[ASN][1000 genomes]
rs10241809	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10242348	0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10246400	0.97[ASN][1000 genomes]
rs10255901	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10256144	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10266879	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10266971	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10272181	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10273647	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10275398	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10275720	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10275779	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10275780	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11760321	0.82[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11762285	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11763432	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11766220	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11770388	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772165	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11772364	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11772424	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11772427	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773187	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11773422	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13437880	0.90[ASN][1000 genomes]
rs4720606	0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4720607	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4720608	0.97[ASN][1000 genomes]
rs4720609	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4720610	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4720611	0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4720612	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724611	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4724612	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59668342	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975915	0.90[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs73107254	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7776882	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7793995	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7794051	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7794346	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7804238	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9690214	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv888003	chr7:47694270-47907214	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1024392	chr7:47707023-47758976	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv1018608	chr7:47708525-47831535	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	nsv1024027	chr7:47709936-47743485	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1022906	chr7:47709936-47831535	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
7	nsv1028355	chr7:47715107-47758976	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10479871	IGFBP1	cis	parietal	SCAN
rs10479871	TNS3	cis	lymphoblastoid	seeQTL
rs10479871	C7orf72	cis	parietal	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:47718600-47728000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr7:47718800-47725600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr7:47720000-47728000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:47720000-47732400	Weak transcription	Spleen	Spleen
5	chr7:47720600-47724200	Weak transcription	K562	blood
6	chr7:47721200-47728000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr7:47721200-47728000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:47721200-47728000	Weak transcription	Brain Substantia Nigra	brain
9	chr7:47721200-47728200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr7:47721600-47727400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr7:47722600-47723600	Flanking Active TSS	HepG2	liver
12	chr7:47722600-47723800	Enhancers	Fetal Intestine Large	intestine
13	chr7:47723000-47723600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr7:47723000-47723600	Enhancers	iPS-15b Cell Line	embryonic stem cell
15	chr7:47723000-47723600	Enhancers	HMEC	breast
16	chr7:47723000-47724000	Weak transcription	Placenta	Placenta
17	chr7:47723200-47723600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr7:47723400-47723800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr7:47723400-47724400	Weak transcription	A549	lung
20	chr7:47723400-47728000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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