Variant report

Variant	rs10861282
Chromosome Location	chr12:105259244-105259245
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105252367..105254848-chr12:105257753..105259443,2	K562	blood:
2	chr12:104581580..104584541-chr12:105258858..105261291,2	K562	blood:
3	chr12:105257620..105260292-chr12:105262517..105265546,3	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10507183	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.80[YRI][hapmap];0.94[ASN][1000 genomes]
rs10507185	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10778354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10778356	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861278	0.90[ASN][1000 genomes]
rs10861280	0.90[ASN][1000 genomes]
rs10861291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861293	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861295	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861297	0.91[ASN][1000 genomes]
rs11112208	0.94[CHB][hapmap];0.90[ASN][1000 genomes]
rs11112221	0.90[ASN][1000 genomes]
rs11112234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12230637	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17828033	0.82[ASN][1000 genomes]
rs17829927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2047126	0.89[ASN][1000 genomes]
rs2245695	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2249941	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2252843	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2264883	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2264893	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2453163	0.91[ASN][1000 genomes]
rs2453164	0.91[ASN][1000 genomes]
rs2453169	0.93[CHB][hapmap];0.88[JPT][hapmap];0.92[ASN][1000 genomes]
rs2463430	0.88[ASN][1000 genomes]
rs2468088	0.87[ASN][1000 genomes]
rs2468094	0.90[ASN][1000 genomes]
rs2468096	0.90[ASN][1000 genomes]
rs2468098	0.90[ASN][1000 genomes]
rs2468103	0.91[ASN][1000 genomes]
rs2468107	0.94[CHB][hapmap];0.91[ASN][1000 genomes]
rs2468108	0.91[ASN][1000 genomes]
rs2468336	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2468338	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs2468339	0.94[CHB][hapmap];0.89[ASN][1000 genomes]
rs2468341	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[ASN][1000 genomes]
rs2468342	0.88[ASN][1000 genomes]
rs2468343	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.80[MEX][hapmap];0.91[ASN][1000 genomes]
rs2468344	0.87[ASN][1000 genomes]
rs2468345	0.87[ASN][1000 genomes]
rs2468396	0.87[EUR][1000 genomes]
rs2468397	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2642119	0.91[ASN][1000 genomes]
rs2642120	0.94[CHB][hapmap];0.91[ASN][1000 genomes]
rs2730294	0.94[CHB][hapmap];0.81[JPT][hapmap];0.91[ASN][1000 genomes]
rs3890816	0.84[CEU][hapmap]
rs4076550	0.82[YRI][hapmap]
rs4130161	0.87[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4257060	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4537841	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4630370	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4644704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4964116	0.88[CEU][hapmap]
rs7959777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7961766	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7971260	0.91[ASN][1000 genomes]
rs7971392	0.92[ASN][1000 genomes]
rs9705471	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10861282	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105220800-105260600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105238400-105260400	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr12:105238400-105280000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:105243800-105265800	Weak transcription	Fetal Stomach	stomach
5	chr12:105248000-105269000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr12:105248800-105259600	Strong transcription	Liver	Liver
7	chr12:105257000-105259400	Enhancers	Ovary	ovary
8	chr12:105257000-105260000	Enhancers	NHDF-Ad	bronchial
9	chr12:105257000-105260600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr12:105257000-105260800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr12:105257000-105260800	Enhancers	Muscle Satellite Cultured Cells	--
12	chr12:105257000-105261400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr12:105257600-105260000	Weak transcription	HSMMtube	muscle
14	chr12:105257600-105260400	Enhancers	Hela-S3	cervix
15	chr12:105257800-105259400	Enhancers	Right Atrium	heart
16	chr12:105257800-105259800	Weak transcription	NH-A	brain
17	chr12:105258000-105259400	Enhancers	Primary hematopoietic stem cells short term culture	blood
18	chr12:105258200-105260000	Enhancers	Primary monocytes fromperipheralblood	blood
19	chr12:105258400-105260000	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr12:105258600-105259400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr12:105258600-105259400	Enhancers	HMEC	breast
22	chr12:105258600-105259600	Enhancers	NHEK	skin
23	chr12:105258600-105259800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:105258600-105259800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:105258600-105260000	Enhancers	GM12878-XiMat	blood
26	chr12:105258600-105260800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr12:105258800-105259400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr12:105258800-105259400	Enhancers	Fetal Thymus	thymus
29	chr12:105258800-105259400	Enhancers	Pancreas	Pancrea
30	chr12:105258800-105259600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr12:105258800-105260200	Enhancers	Breast Myoepithelial Primary Cells	Breast
32	chr12:105259000-105259400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:105259000-105259800	Enhancers	Dnd41	blood
34	chr12:105259200-105259400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:105259200-105259400	Enhancers	Placenta	Placenta
36	chr12:105259200-105259600	Weak transcription	Osteobl	bone
37	chr12:105259200-105260000	Weak transcription	A549	lung
38	chr12:105259200-105263800	Weak transcription	Aorta	Aorta
39	chr12:105259200-105264400	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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