Variant report

Variant	rs10254839
Chromosome Location	chr7:69791367-69791368
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10229027	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10229155	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10234614	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10234844	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10234892	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10237530	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10237685	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10244275	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10246631	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10251306	0.85[ASN][1000 genomes]
rs10251416	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10256062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10256186	0.86[ASN][1000 genomes]
rs10258298	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10258962	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10277411	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10280622	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10486874	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10486875	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10499812	0.86[ASN][1000 genomes]
rs10950199	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766329	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12112638	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12155138	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12374873	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698866	0.86[ASN][1000 genomes]
rs12698877	0.89[ASN][1000 genomes]
rs12698895	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698896	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698897	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12698899	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13221252	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13226923	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1357759	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1404274	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464786	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1464787	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1464788	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1524518	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1880368	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2103132	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2222544	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2280613	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2280614	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2866277	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35303761	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3846984	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6460541	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6460542	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6460543	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6943555	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6953344	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6954715	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6954837	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6957740	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967697	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6967986	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6969375	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6976581	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7781035	0.91[ASN][1000 genomes]
rs7781401	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7781727	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7787612	0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7788024	0.91[ASN][1000 genomes]
rs7790934	0.91[ASN][1000 genomes]
rs7792775	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7792964	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7798991	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7799308	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7808540	0.91[ASN][1000 genomes]
rs8180850	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9638268	0.82[ASN][1000 genomes]
rs9918496	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9918544	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[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	nsv1018749	chr7:69149029-69995112	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv532782	chr7:69383651-70189959	Weak transcription Genic enhancers Enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv869342	chr7:69671501-69958576	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv607431	chr7:69699074-69828729	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv888337	chr7:69707076-69952187	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv529669	chr7:69709373-69974708	Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv1028870	chr7:69742438-69879231	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10254839	WBSCR17	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:69779600-69802200	Weak transcription	Primary B cells from cord blood	blood
2	chr7:69790000-69791800	Enhancers	NHEK	skin
3	chr7:69790400-69791400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr7:69790400-69791400	Enhancers	Osteobl	bone
5	chr7:69790400-69791600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr7:69790400-69791600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr7:69790400-69791600	Enhancers	Muscle Satellite Cultured Cells	--
8	chr7:69790400-69791600	Enhancers	NHLF	lung
9	chr7:69790400-69791800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr7:69790400-69791800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr7:69790400-69791800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr7:69790400-69791800	Enhancers	HMEC	breast
13	chr7:69790400-69791800	Enhancers	NHDF-Ad	bronchial
14	chr7:69790600-69791400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr7:69790600-69791400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr7:69790600-69791400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr7:69790600-69791400	Enhancers	Placenta Amnion	Placenta Amnion
18	chr7:69790600-69791400	Enhancers	HSMMtube	muscle
19	chr7:69790600-69791400	Enhancers	NH-A	brain
20	chr7:69790600-69791600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr7:69790600-69791600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr7:69790600-69791600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr7:69790600-69791600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:69790600-69791600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr7:69790600-69791600	Enhancers	Fetal Brain Male	brain
26	chr7:69790600-69791600	Enhancers	Dnd41	blood
27	chr7:69790600-69791600	Enhancers	HSMM	muscle
28	chr7:69790800-69791400	Enhancers	Fetal Stomach	stomach
29	chr7:69790800-69791400	Enhancers	Fetal Thymus	thymus
30	chr7:69791000-69791400	Enhancers	Primary hematopoietic stem cells	blood
31	chr7:69791200-69791400	Enhancers	Fetal Muscle Leg	muscle

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