Variant report

Variant	rs10875731
Chromosome Location	chr12:48432743-48432744
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:48422786..48426072-chr12:48430482..48433177,3	MCF-7	breast:
2	chr12:48431984..48434939-chr12:48438010..48440362,2	K562	blood:
3	chr12:48416195..48418689-chr12:48432533..48434686,2	K562	blood:

Extended variants
information (count: 77 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10875720	0.91[ASN][1000 genomes]
rs10875722	0.91[ASN][1000 genomes]
rs10875723	0.92[ASN][1000 genomes]
rs10875724	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10875725	0.98[ASN][1000 genomes]
rs10875728	0.96[EUR][1000 genomes]
rs10875729	0.96[EUR][1000 genomes]
rs10875730	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875732	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10875735	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10875736	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs10875737	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10875738	0.83[EUR][1000 genomes]
rs10875740	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs10875747	0.82[EUR][1000 genomes]
rs10875748	0.82[EUR][1000 genomes]
rs11168355	0.90[ASN][1000 genomes]
rs11168357	0.92[ASN][1000 genomes]
rs11168369	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168370	0.98[EUR][1000 genomes]
rs11168371	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168374	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11168383	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168386	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11168401	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs11168403	0.81[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs11168414	0.83[EUR][1000 genomes]
rs11168418	0.82[EUR][1000 genomes]
rs11168420	0.83[EUR][1000 genomes]
rs11168422	0.80[EUR][1000 genomes]
rs12296244	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12297004	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12301339	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12304476	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12305182	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12306451	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs12310999	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12311774	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12311953	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12313300	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12313404	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12315625	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs17122620	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17122666	0.82[EUR][1000 genomes]
rs2079295	0.90[ASN][1000 genomes]
rs2158516	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2228500	0.82[EUR][1000 genomes]
rs2269935	0.82[EUR][1000 genomes]
rs2269936	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286021	0.82[EUR][1000 genomes]
rs28459711	0.91[ASN][1000 genomes]
rs3782910	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs3782911	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs4760609	0.93[ASN][1000 genomes]
rs4760610	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4760676	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4760680	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4760681	0.83[EUR][1000 genomes]
rs58952582	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs60761335	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61918774	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61918806	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61918809	0.81[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs61918810	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs719008	0.91[ASN][1000 genomes]
rs725454	0.83[EUR][1000 genomes]
rs7299135	0.91[ASN][1000 genomes]
rs7299271	0.91[ASN][1000 genomes]
rs7299364	0.91[ASN][1000 genomes]
rs73102065	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs73102067	0.81[AFR][1000 genomes]
rs7964359	0.82[ASN][1000 genomes]
rs886588	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs989144	0.81[AFR][1000 genomes];0.83[EUR][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
rs10875731	RP1-228P16.1	cis	Adipose Subcutaneous	GTEx
rs10875731	RP1-228P16.1	cis	Skin Sun Exposed Lower leg	GTEx
rs10875731	RP1-228P16.1	cis	Heart Left Ventricle	GTEx
rs10875731	RP1-228P16.1	cis	Thyroid	GTEx
rs10875731	RP1-228P16.1	cis	Artery Tibial	GTEx

Chromatin state (count:74 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48422800-48438800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:48424800-48437400	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:48427600-48435600	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr12:48429000-48434200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr12:48429200-48433600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:48429200-48437000	Weak transcription	GM12878-XiMat	blood
7	chr12:48429400-48433200	Weak transcription	Colonic Mucosa	Colon
8	chr12:48429400-48435400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr12:48429600-48436400	Weak transcription	HMEC	breast
10	chr12:48429800-48434200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr12:48430200-48433200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:48430800-48432800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:48431200-48433200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr12:48431400-48436600	Weak transcription	Muscle Satellite Cultured Cells	--
15	chr12:48431400-48438200	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:48431400-48438400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr12:48431600-48437800	Weak transcription	Brain Germinal Matrix	brain
18	chr12:48431800-48435600	Weak transcription	Primary hematopoietic stem cells	blood
19	chr12:48431800-48435800	Weak transcription	Primary B cells from cord blood	blood
20	chr12:48431800-48436000	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:48431800-48436400	Weak transcription	Fetal Muscle Trunk	muscle
22	chr12:48431800-48436400	Weak transcription	Placenta	Placenta
23	chr12:48431800-48437000	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr12:48431800-48437000	Weak transcription	Liver	Liver
25	chr12:48431800-48437600	Weak transcription	Adipose Nuclei	Adipose
26	chr12:48431800-48438200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr12:48431800-48438200	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr12:48431800-48438200	Weak transcription	Fetal Stomach	stomach
29	chr12:48431800-48438200	Weak transcription	Lung	lung
30	chr12:48431800-48438200	Weak transcription	Pancreas	Pancrea
31	chr12:48431800-48438400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr12:48431800-48438400	Weak transcription	K562	blood
33	chr12:48431800-48438800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr12:48431800-48456600	Weak transcription	NHLF	lung
35	chr12:48432000-48433000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:48432000-48433000	Weak transcription	Fetal Intestine Small	intestine
37	chr12:48432000-48433000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr12:48432000-48435800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:48432000-48436000	Weak transcription	Fetal Thymus	thymus
40	chr12:48432000-48436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:48432000-48436400	Weak transcription	Brain Angular Gyrus	brain
42	chr12:48432000-48436400	Weak transcription	Fetal Lung	lung
43	chr12:48432000-48436400	Weak transcription	HSMM	muscle
44	chr12:48432000-48436800	Weak transcription	NH-A	brain
45	chr12:48432000-48437000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr12:48432000-48438200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr12:48432000-48438200	Weak transcription	Right Ventricle	heart
48	chr12:48432000-48438200	Weak transcription	Spleen	Spleen
49	chr12:48432000-48438400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr12:48432000-48438400	Weak transcription	Fetal Kidney	kidney

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