Variant report

Variant	rs10875735
Chromosome Location	chr12:48463806-48463807
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:48463736..48464295-chr2:203696481..203696981,2	NB4	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10219623	0.85[AMR][1000 genomes]
rs10875724	0.82[CEU][hapmap]
rs10875725	0.82[ASN][1000 genomes]
rs10875730	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875731	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875732	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875736	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10875737	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875738	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10875740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10875745	0.85[AMR][1000 genomes]
rs10875746	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10875747	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875748	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10875750	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10875756	0.82[EUR][1000 genomes]
rs10875767	0.84[CEU][hapmap]
rs10875770	0.83[CEU][hapmap]
rs10875772	0.83[CEU][hapmap]
rs11168369	0.92[CEU][hapmap];0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168370	0.82[EUR][1000 genomes]
rs11168371	1.00[CEU][hapmap];0.83[ASN][1000 genomes]
rs11168374	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168383	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168386	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168403	0.92[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11168413	0.85[AMR][1000 genomes]
rs11168414	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11168418	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11168420	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs11168422	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11168427	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11168433	0.92[CEU][hapmap];0.82[EUR][1000 genomes]
rs11168459	0.83[CEU][hapmap]
rs12296244	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12297004	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297470	0.85[AMR][1000 genomes]
rs12301339	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12304476	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12305182	0.82[CEU][hapmap]
rs12305511	0.85[CEU][hapmap]
rs12306451	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12310813	0.85[AMR][1000 genomes]
rs12310999	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12311774	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311953	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313404	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12315625	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17122620	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17122666	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17122812	0.81[CEU][hapmap]
rs1859445	0.85[AMR][1000 genomes]
rs2107638	0.85[AMR][1000 genomes]
rs2158516	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2228500	0.92[CEU][hapmap];0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2269935	0.92[CEU][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2269936	0.91[CEU][hapmap];0.81[AFR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2286021	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3782910	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3782911	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4760622	0.85[CEU][hapmap]
rs4760680	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4760681	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4760689	0.82[EUR][1000 genomes]
rs4760690	0.82[EUR][1000 genomes]
rs4760695	0.85[CEU][hapmap]
rs58952582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60761335	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918774	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61918806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61918809	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61918810	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs725454	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73102065	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73102067	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485355	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8804	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs886588	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs989144	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	esv2758307	chr12:48429702-48825499	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	esv2759898	chr12:48429702-48825499	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs10875735	RP1-228P16.1	cis	Thyroid	GTEx
rs10875735	RP1-228P16.1	cis	Artery Tibial	GTEx
rs10875735	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875735	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs10875735	RP1-228P16.1	cis	Heart Left Ventricle	GTEx

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48432200-48498400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:48435200-48476200	Weak transcription	Stomach Mucosa	stomach
3	chr12:48437200-48489000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr12:48439200-48468000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:48441400-48482600	Weak transcription	Small Intestine	intestine
6	chr12:48441600-48468000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48443000-48478800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr12:48444200-48474600	Weak transcription	Gastric	stomach
9	chr12:48444800-48468000	Weak transcription	Spleen	Spleen
10	chr12:48449400-48464400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr12:48452000-48468600	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr12:48452000-48468800	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr12:48452000-48468800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:48452000-48469400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr12:48452200-48468600	Strong transcription	NH-A	brain
16	chr12:48452200-48468800	Strong transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:48452200-48469000	Strong transcription	Primary monocytes fromperipheralblood	blood
18	chr12:48452200-48469600	Strong transcription	Primary T helper cells fromperipheralblood	blood
19	chr12:48452200-48470000	Strong transcription	Placenta	Placenta
20	chr12:48452400-48468800	Strong transcription	Adipose Nuclei	Adipose
21	chr12:48452400-48468800	Strong transcription	Duodenum Mucosa	Duodenum
22	chr12:48452400-48468800	Strong transcription	Fetal Thymus	thymus
23	chr12:48452400-48469600	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr12:48452600-48468400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:48452800-48468000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:48452800-48468600	Strong transcription	Duodenum Smooth Muscle	Duodenum
27	chr12:48453000-48464800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:48453000-48468400	Strong transcription	Fetal Lung	lung
29	chr12:48453000-48468800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:48453000-48469200	Weak transcription	Fetal Heart	heart
31	chr12:48453000-48498200	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr12:48453200-48469200	Strong transcription	Primary T cells fromperipheralblood	blood
33	chr12:48453600-48469800	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr12:48453600-48471200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:48453800-48466000	Weak transcription	Esophagus	oesophagus
36	chr12:48453800-48469000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr12:48453800-48469000	Strong transcription	Primary B cells from peripheral blood	blood
38	chr12:48453800-48469000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr12:48453800-48469000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr12:48453800-48469400	Strong transcription	A549	lung
41	chr12:48453800-48474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr12:48454000-48469000	Strong transcription	Liver	Liver
43	chr12:48454000-48494000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr12:48454600-48469000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:48454600-48478800	Weak transcription	Pancreas	Pancrea
46	chr12:48454800-48472000	Strong transcription	Dnd41	blood
47	chr12:48455600-48464400	Weak transcription	Lung	lung
48	chr12:48455600-48469000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:48456200-48469600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
50	chr12:48457200-48466000	Weak transcription	Colonic Mucosa	Colon

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