Variant report

Variant	rs2062499
Chromosome Location	chr3:177391196-177391197
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NFE2	chr3:177391186-177391522	K562	blood:	n/a	chr3:177391352-177391367 chr3:177391353-177391362
2	ATF1	chr3:177391194-177391497	K562	blood:	n/a	n/a
3	TAL1	chr3:177390030-177391545	K562	blood:	n/a	chr3:177390650-177390658
4	JUND	chr3:177390989-177391578	K562	blood:	n/a	n/a
5	CBX3	chr3:177391170-177391815	K562	blood:	n/a	n/a
6	RAD21	chr3:177391163-177391559	IMR90	lung:	n/a	n/a
7	CEBPB	chr3:177391160-177391441	IMR90	lung:	n/a	n/a
8	MAFK	chr3:177391164-177391636	IMR90	lung:	n/a	chr3:177391354-177391363
9	MAFK	chr3:177390956-177391554	K562	blood:	n/a	chr3:177391354-177391363
10	BACH1	chr3:177391146-177391645	K562	blood:	n/a	n/a
11	MAFF	chr3:177391103-177391626	K562	blood:	n/a	n/a
12	TEAD4	chr3:177391081-177391607	K562	blood:	n/a	n/a

Variant related genes	Relation type
LINC00578	TF binding region

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10513748	0.88[ASN][1000 genomes]
rs10513749	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10513750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10936953	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs10936954	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12487312	0.83[ASN][1000 genomes]
rs12487458	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12489304	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12489969	0.82[ASN][1000 genomes]
rs13059117	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13059514	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs13060224	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13060502	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13071785	0.83[ASN][1000 genomes]
rs13082519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13097723	0.82[ASN][1000 genomes]
rs13340118	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13340167	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13340172	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1499810	0.84[ASN][1000 genomes]
rs1500047	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1604032	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1846628	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2062500	0.94[CHB][hapmap];0.83[ASN][1000 genomes]
rs28700961	0.81[ASN][1000 genomes]
rs28711160	0.81[ASN][1000 genomes]
rs33964414	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34188001	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34491022	0.83[ASN][1000 genomes]
rs34992356	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35791913	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35847814	0.83[ASN][1000 genomes]
rs35868955	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4857725	0.82[ASN][1000 genomes]
rs4857726	0.82[ASN][1000 genomes]
rs56005554	0.82[ASN][1000 genomes]
rs57405296	0.99[ASN][1000 genomes]
rs62283347	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6443481	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6443482	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6765836	0.82[ASN][1000 genomes]
rs6772134	0.81[ASN][1000 genomes]
rs6779492	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6793629	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6793647	0.81[ASN][1000 genomes]
rs6798785	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6803889	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs68151580	0.83[ASN][1000 genomes]
rs7610506	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7615900	0.85[ASN][1000 genomes]
rs7639373	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641099	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7644248	0.81[ASN][1000 genomes]
rs7646117	0.85[ASN][1000 genomes]
rs7652174	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs937507	0.88[ASN][1000 genomes]
rs937561	0.84[ASN][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	esv2752972	chr3:176924298-177425298	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	nsv931055	chr3:177229521-177889872	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv4131	chr3:177366549-177399301	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2062499	KCNMB2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:177383800-177391400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr3:177383800-177397800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:177389000-177392400	Enhancers	K562	blood
4	chr3:177389800-177391800	Enhancers	Fetal Intestine Large	intestine
5	chr3:177390200-177391600	Enhancers	NHLF	lung
6	chr3:177390400-177391200	Enhancers	Brain Germinal Matrix	brain
7	chr3:177390400-177391200	Enhancers	Right Atrium	heart
8	chr3:177390400-177392200	Enhancers	Osteobl	bone
9	chr3:177390400-177392400	Enhancers	NHDF-Ad	bronchial
10	chr3:177390600-177391600	Weak transcription	Liver	Liver
11	chr3:177390600-177391800	Enhancers	Brain Anterior Caudate	brain
12	chr3:177390600-177391800	Enhancers	Brain Inferior Temporal Lobe	brain
13	chr3:177390600-177391800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:177390600-177391800	Enhancers	HSMMtube	muscle
15	chr3:177390600-177392200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr3:177390600-177392400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:177390600-177392400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:177390600-177392600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr3:177390600-177392800	Enhancers	Fetal Brain Male	brain
20	chr3:177390600-177393200	Enhancers	Primary hematopoietic stem cells short term culture	blood
21	chr3:177390800-177392000	Enhancers	Brain Substantia Nigra	brain
22	chr3:177390800-177392000	Enhancers	Fetal Heart	heart
23	chr3:177390800-177392200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr3:177390800-177392400	Enhancers	Primary hematopoietic stem cells	blood
25	chr3:177390800-177392400	Enhancers	Stomach Smooth Muscle	stomach
26	chr3:177390800-177392600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr3:177390800-177392600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr3:177391000-177391400	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr3:177391000-177391800	Enhancers	Primary monocytes fromperipheralblood	blood
30	chr3:177391000-177391800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr3:177391000-177391800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr3:177391000-177391800	Enhancers	Brain Hippocampus Middle	brain
33	chr3:177391000-177391800	Enhancers	Monocytes-CD14+_RO01746	blood
34	chr3:177391000-177391800	Enhancers	NHEK	skin
35	chr3:177391000-177392000	Enhancers	Brain Cingulate Gyrus	brain
36	chr3:177391000-177392200	Enhancers	Adipose Nuclei	Adipose
37	chr3:177391000-177392200	Enhancers	Brain Angular Gyrus	brain
38	chr3:177391000-177392200	Enhancers	Ovary	ovary
39	chr3:177391000-177392200	Enhancers	Rectal Smooth Muscle	rectum
40	chr3:177391000-177392200	Enhancers	HMEC	breast
41	chr3:177391000-177392400	Enhancers	Colon Smooth Muscle	Colon
42	chr3:177391000-177392400	Enhancers	Psoas Muscle	Psoas
43	chr3:177391000-177392400	Enhancers	Skeletal Muscle Male	skeletal muscle
44	chr3:177391000-177392400	Enhancers	Skeletal Muscle Female	skeletal muscle
45	chr3:177391000-177392400	Enhancers	NH-A	brain
46	chr3:177391000-177392600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:177391000-177392600	Enhancers	Fetal Lung	lung
48	chr3:177391000-177392600	Enhancers	Fetal Muscle Leg	muscle
49	chr3:177391000-177392600	Enhancers	Fetal Thymus	thymus
50	chr3:177391000-177395200	Enhancers	Fetal Kidney	kidney

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