Variant report

Variant	rs12526643
Chromosome Location	chr6:73978949-73978950
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:73978150-73986643..6:74160392-74184826	K562	blood:
2	6:73978150-73986643..6:74062967-74076046	H1-hESC	embryonic stem cell:	embryo
3	6:73978150-73986643..6:74099986-74112890	H1-hESC	embryonic stem cell:	embryo
4	6:73978150-73986643..6:74078047-74099067	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000203909	Chromatin interaction
ENSG00000231332	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000135297	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000224221	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10455092	0.93[ASN][1000 genomes]
rs10455273	0.93[ASN][1000 genomes]
rs10455274	0.93[ASN][1000 genomes]
rs1066687	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12153835	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12203663	0.93[ASN][1000 genomes]
rs12208781	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12210531	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12216162	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529624	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529658	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12530029	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12530079	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13194683	0.91[ASN][1000 genomes]
rs13212903	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13213885	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13219250	0.93[ASN][1000 genomes]
rs1555443	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1869559	0.95[ASN][1000 genomes]
rs1970551	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1974368	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2124004	0.91[ASN][1000 genomes]
rs2168113	0.95[ASN][1000 genomes]
rs2254630	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2603471	0.96[ASN][1000 genomes]
rs2797086	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28530192	0.93[ASN][1000 genomes]
rs2984129	0.93[ASN][1000 genomes]
rs34246858	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34531450	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34637067	0.93[ASN][1000 genomes]
rs34821383	0.93[ASN][1000 genomes]
rs35664677	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4706533	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4706534	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4708041	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4708042	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs471270	0.96[ASN][1000 genomes]
rs471938	0.93[ASN][1000 genomes]
rs502107	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs502282	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs509406	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs510551	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs511219	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs512366	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs555779	0.91[ASN][1000 genomes]
rs57113415	0.84[ASN][1000 genomes]
rs573535	0.93[ASN][1000 genomes]
rs576229	0.91[ASN][1000 genomes]
rs579736	0.96[ASN][1000 genomes]
rs61493410	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62438232	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438233	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438235	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62438239	0.90[ASN][1000 genomes]
rs66984567	0.93[ASN][1000 genomes]
rs6923111	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6923734	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7382700	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7740081	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7742847	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7743609	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7744174	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7758047	0.95[ASN][1000 genomes]
rs7759043	0.95[ASN][1000 genomes]
rs7759315	0.95[ASN][1000 genomes]
rs7764719	0.89[ASN][1000 genomes]
rs7765618	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7769905	0.87[ASN][1000 genomes]
rs9800483	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9800824	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv1030079	chr6:73920050-73984084	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12526643	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx
rs12526643	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973400-73985000	Weak transcription	Small Intestine	intestine
2	chr6:73973400-73986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr6:73973400-74000400	Weak transcription	Aorta	Aorta
4	chr6:73973600-73983400	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr6:73973600-73984400	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr6:73973600-73985400	Weak transcription	Left Ventricle	heart
7	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr6:73973600-74018600	Weak transcription	A549	lung
9	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr6:73973800-73980600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:73973800-73983400	Weak transcription	Placenta	Placenta
12	chr6:73973800-73985200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr6:73973800-73995600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:73973800-73995600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:73973800-74000400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr6:73974000-73980600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr6:73974000-73980600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr6:73974000-73983800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr6:73974000-73983800	Weak transcription	Osteobl	bone
20	chr6:73974000-73985000	Weak transcription	Lung	lung
21	chr6:73974000-73995600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:73974000-74000400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr6:73974000-74009000	Weak transcription	HSMM	muscle
24	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr6:73974200-73983400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:73974200-73992600	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:73974400-73980800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr6:73974400-73983600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:73974400-73983600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:73974400-73983600	Weak transcription	Ovary	ovary
31	chr6:73974400-73984000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr6:73974400-73986000	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr6:73974400-73986200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr6:73974400-73986600	Weak transcription	Pancreas	Pancrea
35	chr6:73974400-73986800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr6:73974400-73986800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr6:73974400-73986800	Weak transcription	Spleen	Spleen
38	chr6:73974400-73987000	Weak transcription	Primary B cells from cord blood	blood
39	chr6:73974400-74000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr6:73974400-74000400	Weak transcription	NHDF-Ad	bronchial
41	chr6:73974400-74008800	Weak transcription	NH-A	brain
42	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr6:73974600-73980000	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr6:73974600-73981800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr6:73974600-73985200	Weak transcription	Primary B cells from peripheral blood	blood
46	chr6:73974600-73986000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr6:73974600-73986200	Weak transcription	Esophagus	oesophagus
48	chr6:73974600-73986400	Weak transcription	Gastric	stomach
49	chr6:73974600-73986600	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr6:73974600-73987000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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