Variant report

Variant	rs10400824
Chromosome Location	chr15:42951277-42951278
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 74 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10162939	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1197548	0.93[EUR][1000 genomes]
rs1197549	0.93[EUR][1000 genomes]
rs1197550	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1197551	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12102055	0.86[EUR][1000 genomes]
rs1212814	0.86[EUR][1000 genomes]
rs12906497	0.82[EUR][1000 genomes]
rs12912064	0.82[EUR][1000 genomes]
rs12917018	0.82[EUR][1000 genomes]
rs16957020	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16957091	0.81[EUR][1000 genomes]
rs16957104	0.83[EUR][1000 genomes]
rs1705356	0.93[EUR][1000 genomes]
rs1915241	0.80[EUR][1000 genomes]
rs1995939	0.86[EUR][1000 genomes]
rs2136900	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2175370	0.97[AFR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2280048	0.85[EUR][1000 genomes]
rs2305084	0.86[EUR][1000 genomes]
rs2305085	0.83[ASN][1000 genomes]
rs2412740	0.85[EUR][1000 genomes]
rs28479391	0.88[EUR][1000 genomes]
rs28549876	0.82[EUR][1000 genomes]
rs28562951	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28744617	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28798437	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28811114	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28823029	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3099758	0.93[EUR][1000 genomes]
rs3106285	0.83[EUR][1000 genomes]
rs3106286	0.86[EUR][1000 genomes]
rs3199486	0.86[EUR][1000 genomes]
rs34603230	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs35738819	0.80[EUR][1000 genomes]
rs3742987	0.83[EUR][1000 genomes]
rs3742993	0.82[EUR][1000 genomes]
rs4265781	0.82[EUR][1000 genomes]
rs4545789	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4924690	0.94[EUR][1000 genomes]
rs4924691	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924692	0.87[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4924694	0.83[ASN][1000 genomes]
rs57298545	0.85[EUR][1000 genomes]
rs623271	0.93[EUR][1000 genomes]
rs6493059	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6493063	0.85[EUR][1000 genomes]
rs67391479	0.80[EUR][1000 genomes]
rs7163030	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7166373	0.80[EUR][1000 genomes]
rs7167392	0.84[EUR][1000 genomes]
rs7169009	0.82[EUR][1000 genomes]
rs7169202	0.93[EUR][1000 genomes]
rs7175582	0.88[EUR][1000 genomes]
rs7182141	0.85[EUR][1000 genomes]
rs8023524	0.83[ASN][1000 genomes]
rs8024902	0.92[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8026233	0.82[EUR][1000 genomes]
rs8027427	0.82[EUR][1000 genomes]
rs8031218	0.82[EUR][1000 genomes]
rs8034664	0.83[EUR][1000 genomes]
rs8039711	0.97[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8039765	0.85[EUR][1000 genomes]
rs8043472	0.93[EUR][1000 genomes]
rs9269	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs938047	0.85[EUR][1000 genomes]
rs9783713	0.88[EUR][1000 genomes]
rs9919994	0.88[EUR][1000 genomes]
rs9920163	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9944248	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42898000-42967800	Weak transcription	Fetal Intestine Small	intestine
2	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
3	chr15:42909600-42966400	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:42923000-42958200	Weak transcription	Hela-S3	cervix
5	chr15:42925200-42966000	Weak transcription	NH-A	brain
6	chr15:42925200-42966800	Weak transcription	NHLF	lung
7	chr15:42925600-42961000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:42928200-42973600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr15:42928200-42974000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:42930600-42964000	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:42930800-42957400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:42931200-42954600	Weak transcription	Placenta	Placenta
13	chr15:42931200-42963400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr15:42931400-42955800	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr15:42931600-42953600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr15:42931600-42955400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:42931800-42955000	Weak transcription	Fetal Lung	lung
18	chr15:42931800-42955000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:42931800-42955600	Weak transcription	Lung	lung
20	chr15:42931800-42957200	Weak transcription	Primary B cells from cord blood	blood
21	chr15:42931800-42958200	Weak transcription	Brain Angular Gyrus	brain
22	chr15:42931800-42968000	Weak transcription	HSMM	muscle
23	chr15:42932000-42958400	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr15:42932200-42966200	Weak transcription	Primary B cells from peripheral blood	blood
25	chr15:42932400-42960000	Weak transcription	Primary T cells from cord blood	blood
26	chr15:42932600-42953200	Weak transcription	Fetal Intestine Large	intestine
27	chr15:42932600-42955400	Weak transcription	Aorta	Aorta
28	chr15:42932800-42953000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr15:42932800-42954000	Weak transcription	Brain Germinal Matrix	brain
30	chr15:42934800-42953000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:42939200-42961200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr15:42940400-42967800	Weak transcription	HepG2	liver
33	chr15:42942800-42955000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr15:42942800-42955400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr15:42942800-42955600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:42942800-42955800	Weak transcription	Brain Substantia Nigra	brain
37	chr15:42942800-42967200	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr15:42942800-42973600	Weak transcription	Psoas Muscle	Psoas
39	chr15:42943000-42957600	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:42945000-42953200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:42945000-42955000	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:42945000-42955400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:42945200-42955000	Weak transcription	Left Ventricle	heart
44	chr15:42945200-42955400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:42945200-42973400	Weak transcription	Thymus	Thymus
46	chr15:42945400-42954800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:42945400-42957000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
48	chr15:42945600-42953200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:42945600-42953400	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:42945800-42952800	Weak transcription	Duodenum Smooth Muscle	Duodenum

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