Variant report

Variant	rs1058846
Chromosome Location	chr15:43012024-43012025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:43011244..43015007-chr15:43016381..43019349,5	K562	blood:
2	chr15:43007397..43009798-chr15:43011681..43013458,2	MCF-7	breast:
3	chr15:43010693..43013698-chr15:43016416..43019349,5	K562	blood:
4	chr15:43010972..43017152-chr15:43019499..43025146,7	MCF-7	breast:
5	chr15:43011390..43013542-chr15:43022490..43025034,3	K562	blood:

Variant related genes	Relation type
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 88 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10162939	0.83[CEU][hapmap]
rs11638835	0.85[EUR][1000 genomes]
rs1197550	0.83[CEU][hapmap]
rs1197551	0.83[CEU][hapmap]
rs12594855	0.88[CEU][hapmap]
rs12902830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12903762	0.90[EUR][1000 genomes]
rs12905385	0.89[CEU][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs12905592	0.82[EUR][1000 genomes]
rs12907826	0.84[EUR][1000 genomes]
rs12908349	1.00[ASN][1000 genomes]
rs12911585	0.94[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12913618	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12914380	1.00[ASN][1000 genomes]
rs12914570	0.83[CEU][hapmap]
rs12915116	0.89[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957020	0.82[CEU][hapmap]
rs1705356	0.83[CEU][hapmap]
rs17774047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136899	0.94[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes]
rs2136900	0.84[CEU][hapmap]
rs2136901	0.85[EUR][1000 genomes]
rs2175370	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs2305085	0.82[CEU][hapmap];0.87[EUR][1000 genomes]
rs2412741	0.85[EUR][1000 genomes]
rs3099758	0.83[CEU][hapmap]
rs34191150	0.85[EUR][1000 genomes]
rs34603230	0.87[EUR][1000 genomes]
rs34745458	1.00[ASN][1000 genomes]
rs35088691	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35202249	1.00[ASN][1000 genomes]
rs35298309	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35392023	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35538776	0.89[CEU][hapmap];1.00[CHB][hapmap];0.96[GIH][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs35616173	0.85[EUR][1000 genomes]
rs35738819	0.81[EUR][1000 genomes]
rs36092914	1.00[ASN][1000 genomes]
rs3742988	0.85[EUR][1000 genomes]
rs3742993	0.94[CEU][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.89[EUR][1000 genomes]
rs4545789	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs4923950	0.82[EUR][1000 genomes]
rs4923954	1.00[ASN][1000 genomes]
rs4924690	0.83[CEU][hapmap]
rs4924691	0.83[CEU][hapmap]
rs4924692	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs4924694	0.94[CEU][hapmap];0.91[MEX][hapmap];0.90[EUR][1000 genomes]
rs4924699	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.91[YRI][hapmap];1.00[ASN][1000 genomes]
rs4994112	0.84[CEU][hapmap]
rs57298545	0.86[EUR][1000 genomes]
rs57481952	0.81[AFR][1000 genomes]
rs58938096	0.90[EUR][1000 genomes]
rs61122145	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs623271	0.83[CEU][hapmap]
rs6493059	0.83[CEU][hapmap]
rs6493060	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs6493061	0.89[CEU][hapmap];0.83[EUR][1000 genomes]
rs6493062	0.86[EUR][1000 genomes]
rs66681258	0.88[EUR][1000 genomes]
rs66932813	1.00[ASN][1000 genomes]
rs672054	0.94[CEU][hapmap];0.80[EUR][1000 genomes]
rs71474496	0.88[EUR][1000 genomes]
rs7166373	0.94[CEU][hapmap];0.81[EUR][1000 genomes]
rs7174041	0.82[EUR][1000 genomes]
rs7176860	0.90[EUR][1000 genomes]
rs7182479	0.85[EUR][1000 genomes]
rs7183487	0.90[EUR][1000 genomes]
rs72713784	1.00[ASN][1000 genomes]
rs72713795	1.00[ASN][1000 genomes]
rs72719486	1.00[ASN][1000 genomes]
rs731984	0.84[EUR][1000 genomes]
rs8023524	0.89[CEU][hapmap];0.87[EUR][1000 genomes]
rs8024902	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs8030587	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs8031218	0.88[CEU][hapmap];0.91[MEX][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs8034447	0.85[EUR][1000 genomes]
rs8037613	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs8039711	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs8039765	0.94[CEU][hapmap];0.91[MEX][hapmap];0.86[EUR][1000 genomes]
rs8043472	0.83[CEU][hapmap]
rs9269	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs938047	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs9920163	0.83[CEU][hapmap]
rs9944248	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1058846	BUB1B	cis	parietal	SCAN
rs1058846	TGM5	cis	lymphoblastoid	seeQTL
rs1058846	CDAN1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42908800-43015000	Weak transcription	Fetal Kidney	kidney
2	chr15:42976600-43015200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:42977000-43016600	Weak transcription	Hela-S3	cervix
4	chr15:42981400-43015000	Weak transcription	HSMM	muscle
5	chr15:42984000-43014800	Weak transcription	K562	blood
6	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr15:42987800-43016400	Weak transcription	Esophagus	oesophagus
8	chr15:42993400-43015400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr15:42997200-43016400	Weak transcription	Pancreas	Pancrea
10	chr15:43000800-43018600	Weak transcription	A549	lung
11	chr15:43001000-43014800	Weak transcription	HUVEC	blood vessel
12	chr15:43004200-43016200	Weak transcription	Psoas Muscle	Psoas
13	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
14	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:43008000-43014000	Strong transcription	Fetal Muscle Leg	muscle
16	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr15:43008200-43013000	Strong transcription	Primary hematopoietic stem cells	blood
18	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
22	chr15:43008600-43012800	Strong transcription	Brain Cingulate Gyrus	brain
23	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
24	chr15:43008800-43012600	Strong transcription	Aorta	Aorta
25	chr15:43008800-43014000	Strong transcription	Rectal Smooth Muscle	rectum
26	chr15:43008800-43014200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr15:43008800-43017200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:43008800-43018400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
29	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
30	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
31	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
32	chr15:43008800-43027200	Strong transcription	Lung	lung
33	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
34	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:43009000-43012800	Strong transcription	Brain Hippocampus Middle	brain
36	chr15:43009000-43012800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:43009000-43013400	Strong transcription	Right Ventricle	heart
38	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
41	chr15:43009200-43012600	Weak transcription	Dnd41	blood
42	chr15:43009200-43013000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:43009200-43014800	Weak transcription	Osteobl	bone
44	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:43009400-43015200	Weak transcription	NHDF-Ad	bronchial
46	chr15:43009400-43015600	Weak transcription	Small Intestine	intestine
47	chr15:43009400-43017400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:43009400-43018200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
49	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
50	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine

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