Variant report

Variant	rs10875724
Chromosome Location	chr12:48420253-48420254
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10082861	0.93[CHB][hapmap];0.91[JPT][hapmap]
rs10219623	0.93[JPT][hapmap]
rs10875720	0.95[ASN][1000 genomes]
rs10875722	0.95[ASN][1000 genomes]
rs10875723	0.96[ASN][1000 genomes]
rs10875725	0.94[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs10875728	0.82[EUR][1000 genomes]
rs10875729	0.82[EUR][1000 genomes]
rs10875730	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875731	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875732	0.91[CEU][hapmap];0.86[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875735	0.82[CEU][hapmap]
rs10875745	0.93[JPT][hapmap]
rs10875746	0.93[JPT][hapmap]
rs10875750	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs10875767	0.86[JPT][hapmap]
rs10875770	0.85[JPT][hapmap]
rs10875772	0.85[JPT][hapmap]
rs11168355	0.84[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11168357	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11168369	0.85[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168370	0.80[EUR][1000 genomes]
rs11168371	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap];0.95[ASN][1000 genomes]
rs11168374	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11168403	0.92[CEU][hapmap];0.94[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	0.85[JPT][hapmap]
rs12296244	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12297470	0.92[JPT][hapmap]
rs12304476	0.84[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap]
rs12305182	1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12305511	0.93[JPT][hapmap]
rs12306451	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs12310813	0.93[JPT][hapmap]
rs12310999	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12312134	0.86[JPT][hapmap]
rs17122666	0.93[JPT][hapmap]
rs17122812	0.86[JPT][hapmap]
rs1859445	0.93[JPT][hapmap]
rs1990028	0.91[EUR][1000 genomes]
rs2012773	0.93[JPT][hapmap]
rs2079295	1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2107638	0.93[JPT][hapmap]
rs2228500	0.93[JPT][hapmap]
rs2269933	0.93[JPT][hapmap]
rs2269935	0.93[JPT][hapmap]
rs2269936	0.84[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28459711	0.95[ASN][1000 genomes]
rs3782910	0.85[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]
rs4760609	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4760610	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4760619	0.93[JPT][hapmap]
rs4760622	0.93[JPT][hapmap]
rs4760676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4760681	0.92[JPT][hapmap]
rs4760687	0.93[JPT][hapmap]
rs4760695	0.93[JPT][hapmap]
rs4760696	0.93[JPT][hapmap]
rs4760697	0.93[JPT][hapmap]
rs61918774	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6580659	0.92[JPT][hapmap]
rs7135779	0.92[JPT][hapmap]
rs719008	0.83[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs725454	0.93[JPT][hapmap]
rs7299135	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7299271	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7299364	0.95[ASN][1000 genomes]
rs7486424	0.93[JPT][hapmap]
rs7964359	0.81[CHB][hapmap];0.86[ASN][1000 genomes]
rs8804	0.93[JPT][hapmap]
rs886588	0.84[CEU][hapmap];0.88[CHB][hapmap];0.93[JPT][hapmap]
rs989144	0.92[CEU][hapmap];0.89[CHB][hapmap];0.93[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10875724	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875724	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875724	RP1-228P16.1	cis	Thyroid	GTEx

Chromatin state (count:22 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48415800-48420400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr12:48416800-48423400	Weak transcription	Right Atrium	heart
3	chr12:48417600-48420800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr12:48417800-48421400	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr12:48417800-48423400	Weak transcription	Fetal Lung	lung
6	chr12:48418000-48422200	Weak transcription	Fetal Heart	heart
7	chr12:48418200-48422200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:48418200-48424200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:48418400-48425800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr12:48418600-48421000	Enhancers	Fetal Intestine Small	intestine
11	chr12:48418600-48425200	Enhancers	Fetal Intestine Large	intestine
12	chr12:48418800-48421000	Weak transcription	Right Ventricle	heart
13	chr12:48419200-48422400	Weak transcription	K562	blood
14	chr12:48419400-48420400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:48419600-48421000	Enhancers	HepG2	liver
16	chr12:48419800-48421400	Enhancers	Fetal Thymus	thymus
17	chr12:48420000-48420400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr12:48420000-48422400	Weak transcription	Colon Smooth Muscle	Colon
19	chr12:48420000-48424200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:48420200-48422800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr12:48420200-48423800	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:48420200-48424200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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