Variant report

Variant	rs2396380
Chromosome Location	chr6:45043557-45043558
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs1023089	0.90[ASN][1000 genomes]
rs1023090	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1041332	0.91[ASN][1000 genomes]
rs1080415	0.84[ASN][1000 genomes]
rs10807318	0.86[ASN][1000 genomes]
rs10807319	0.84[ASN][1000 genomes]
rs10807320	0.82[ASN][1000 genomes]
rs10948198	0.90[ASN][1000 genomes]
rs11968042	0.98[ASN][1000 genomes]
rs12190261	0.92[ASN][1000 genomes]
rs12204678	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12205071	0.91[ASN][1000 genomes]
rs12208023	0.91[ASN][1000 genomes]
rs12208483	0.98[ASN][1000 genomes]
rs12526649	0.86[ASN][1000 genomes]
rs12529490	0.86[ASN][1000 genomes]
rs12529990	0.86[ASN][1000 genomes]
rs1284961	0.89[ASN][1000 genomes]
rs1284965	0.87[ASN][1000 genomes]
rs1284969	0.84[ASN][1000 genomes]
rs1284972	0.88[ASN][1000 genomes]
rs1284973	0.89[ASN][1000 genomes]
rs1284975	0.89[ASN][1000 genomes]
rs1284988	0.93[ASN][1000 genomes]
rs1284992	0.90[ASN][1000 genomes]
rs1285004	0.89[ASN][1000 genomes]
rs1285013	0.86[ASN][1000 genomes]
rs1285014	0.86[ASN][1000 genomes]
rs1285019	0.89[ASN][1000 genomes]
rs1285022	0.89[ASN][1000 genomes]
rs1285023	0.89[ASN][1000 genomes]
rs1285026	0.88[ASN][1000 genomes]
rs1290386	0.89[ASN][1000 genomes]
rs1300126	0.89[ASN][1000 genomes]
rs1304168	0.86[ASN][1000 genomes]
rs13198471	0.81[ASN][1000 genomes]
rs13202529	0.84[ASN][1000 genomes]
rs13207575	0.91[ASN][1000 genomes]
rs13211006	0.81[ASN][1000 genomes]
rs1324531	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1324532	0.87[ASN][1000 genomes]
rs1324537	0.88[ASN][1000 genomes]
rs1324540	0.83[ASN][1000 genomes]
rs1329713	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1329714	0.83[ASN][1000 genomes]
rs1359336	0.91[ASN][1000 genomes]
rs1411148	0.99[ASN][1000 genomes]
rs1555681	0.90[EUR][1000 genomes]
rs1581777	0.84[ASN][1000 genomes]
rs1629542	0.84[ASN][1000 genomes]
rs1748231	0.84[ASN][1000 genomes]
rs1748234	0.84[ASN][1000 genomes]
rs1748235	0.84[ASN][1000 genomes]
rs1748242	0.84[ASN][1000 genomes]
rs1797145	0.84[ASN][1000 genomes]
rs1797147	0.82[ASN][1000 genomes]
rs1886345	0.90[ASN][1000 genomes]
rs1937046	0.95[ASN][1000 genomes]
rs1937047	0.98[ASN][1000 genomes]
rs1971482	0.83[ASN][1000 genomes]
rs2038766	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2093901	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2093903	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2186062	0.89[ASN][1000 genomes]
rs2396375	0.82[ASN][1000 genomes]
rs2396425	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34152708	0.81[ASN][1000 genomes]
rs34251367	0.86[ASN][1000 genomes]
rs35134594	0.86[ASN][1000 genomes]
rs35811020	0.82[ASN][1000 genomes]
rs35817842	0.91[ASN][1000 genomes]
rs3920903	0.99[ASN][1000 genomes]
rs4352679	0.82[ASN][1000 genomes]
rs4398713	0.84[ASN][1000 genomes]
rs4412189	0.89[ASN][1000 genomes]
rs4714836	0.91[ASN][1000 genomes]
rs4714838	0.86[ASN][1000 genomes]
rs4714845	0.83[ASN][1000 genomes]
rs4714847	0.84[ASN][1000 genomes]
rs4714848	0.84[ASN][1000 genomes]
rs56138724	0.99[ASN][1000 genomes]
rs6458418	0.89[ASN][1000 genomes]
rs6458419	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6458420	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6458425	0.89[ASN][1000 genomes]
rs6458427	0.87[ASN][1000 genomes]
rs6458428	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6458430	0.87[ASN][1000 genomes]
rs6899378	0.89[ASN][1000 genomes]
rs6899845	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6901786	0.87[ASN][1000 genomes]
rs6905396	0.89[ASN][1000 genomes]
rs6923436	0.98[ASN][1000 genomes]
rs6925467	0.84[ASN][1000 genomes]
rs6933553	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6937317	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6938316	0.86[ASN][1000 genomes]
rs6941169	0.86[ASN][1000 genomes]
rs7738526	0.89[ASN][1000 genomes]
rs7739928	0.91[ASN][1000 genomes]
rs7742360	0.84[ASN][1000 genomes]
rs7743116	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7745506	0.84[ASN][1000 genomes]
rs7750380	0.91[ASN][1000 genomes]
rs7758031	0.91[ASN][1000 genomes]
rs7763450	0.97[ASN][1000 genomes]
rs7763973	0.91[ASN][1000 genomes]
rs7764102	0.86[ASN][1000 genomes]
rs927658	0.89[ASN][1000 genomes]
rs9296453	0.84[ASN][1000 genomes]
rs9296455	0.82[ASN][1000 genomes]
rs9349309	0.92[ASN][1000 genomes]
rs9349313	0.89[ASN][1000 genomes]
rs9349315	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9357469	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9357470	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9357471	0.92[EUR][1000 genomes]
rs9357478	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9357480	0.84[ASN][1000 genomes]
rs9367214	0.92[ASN][1000 genomes]
rs9369529	0.83[ASN][1000 genomes]
rs9369530	0.91[ASN][1000 genomes]
rs9369533	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9369534	0.91[ASN][1000 genomes]
rs9381361	0.91[ASN][1000 genomes]
rs9381364	0.91[ASN][1000 genomes]
rs9381365	0.90[ASN][1000 genomes]
rs9381366	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9381373	0.87[ASN][1000 genomes]
rs9395063	0.99[ASN][1000 genomes]
rs9395065	0.90[ASN][1000 genomes]
rs9395066	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9395069	0.86[EUR][1000 genomes]
rs9395079	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9395086	0.84[ASN][1000 genomes]
rs9395088	0.82[ASN][1000 genomes]
rs9463076	0.87[ASN][1000 genomes]
rs9463081	0.84[ASN][1000 genomes]
rs9472451	0.84[ASN][1000 genomes]
rs964452	0.88[ASN][1000 genomes]
rs969211	0.91[ASN][1000 genomes]
rs988147	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv885861	chr6:44837356-45043618	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv1028393	chr6:44875558-45822335	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv538211	chr6:44875558-45822335	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
4	nsv1024370	chr6:44878053-45251451	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
5	esv2758051	chr6:44879791-45056758	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv2759423	chr6:44879791-45056758	ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv885862	chr6:44890760-45083966	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	nsv885863	chr6:44890760-45083966	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv885864	chr6:44890760-45198796	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
10	nsv1023018	chr6:44925393-45152912	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
11	nsv538212	chr6:44925393-45152912	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv603008	chr6:44958372-45081821	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	esv2762589	chr6:44982992-45044580	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1026728	chr6:45001948-45126730	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv538213	chr6:45001948-45126730	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv885865	chr6:45012223-45102025	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
17	nsv492309	chr6:45020402-45233484	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2396380	SUPT3H	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:45039800-45044200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr6:45039800-45044600	Enhancers	Muscle Satellite Cultured Cells	--
3	chr6:45040600-45044600	Enhancers	NH-A	brain
4	chr6:45040800-45044000	Enhancers	Osteobl	bone
5	chr6:45041000-45044200	Enhancers	HUVEC	blood vessel
6	chr6:45041400-45043600	Enhancers	HMEC	breast
7	chr6:45041400-45044000	Enhancers	NHEK	skin
8	chr6:45041400-45044600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr6:45041600-45044600	Enhancers	NHDF-Ad	bronchial
10	chr6:45042400-45043600	Enhancers	HSMM	muscle
11	chr6:45042400-45044000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr6:45042600-45044200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr6:45042600-45045800	Weak transcription	Dnd41	blood
14	chr6:45042800-45044200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr6:45043000-45046000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:45043200-45044000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr6:45043400-45043600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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