Variant report

Variant	rs10754538
Chromosome Location	chr1:247352621-247352622
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247348019..247350851-chr1:247351523..247353130,2	K562	blood:

Variant related genes	Relation type
ENSG00000215795	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10754539	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap];0.87[ASN][1000 genomes]
rs10802475	0.98[ASN][1000 genomes]
rs10924944	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10924949	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs10924950	0.96[ASN][1000 genomes]
rs10924951	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs10924952	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10924953	0.99[ASN][1000 genomes]
rs10924954	0.98[ASN][1000 genomes]
rs10924955	0.99[ASN][1000 genomes]
rs10924957	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10924958	0.98[ASN][1000 genomes]
rs10924960	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10924961	0.84[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1115201	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1132779	0.99[ASN][1000 genomes]
rs12025262	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069092	0.96[ASN][1000 genomes]
rs12071728	1.00[CHB][hapmap];0.98[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12089377	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12118895	1.00[CHB][hapmap];0.91[JPT][hapmap];0.99[ASN][1000 genomes]
rs12122649	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12131404	0.91[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12133602	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12133699	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs12133802	1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[ASN][1000 genomes]
rs12239403	1.00[YRI][hapmap]
rs2068050	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2380118	0.98[ASN][1000 genomes]
rs3738444	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3820508	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs3820509	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs4925594	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6426226	1.00[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6426227	0.98[ASN][1000 genomes]
rs6656142	1.00[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs6656343	0.96[ASN][1000 genomes]
rs6660243	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6670847	0.97[ASN][1000 genomes]
rs6676905	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6678604	0.99[ASN][1000 genomes]
rs6687710	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs6704274	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873424	chr1:246991094-247366380	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv1005208	chr1:247037441-247597975	Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv535417	chr1:247094131-247409000	ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
4	nsv1005639	chr1:247094161-247401380	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
5	nsv535418	chr1:247094161-247401380	Active TSS ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	47 gene(s)	inside rSNPs	diseases
6	nsv916236	chr1:247124353-247409065	Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	36 gene(s)	inside rSNPs	diseases
7	nsv948419	chr1:247130577-247400404	ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1012616	chr1:247173851-247365588	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv535420	chr1:247173851-247365588	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
10	nsv1002438	chr1:247173851-247401380	ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv427974	chr1:247184802-247352964	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
12	esv3336179	chr1:247195262-247373269	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
13	nsv833126	chr1:247273084-247476150	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	n/a
14	nsv873433	chr1:247278707-247360368	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
15	nsv873434	chr1:247319489-247360368	Strong transcription ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
16	nsv873435	chr1:247336726-247360368	Weak transcription ZNF genes & repeats Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	n/a
17	nsv873436	chr1:247339064-247385877	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	n/a
18	nsv873437	chr1:247340784-247366380	Strong transcription ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	n/a
19	nsv873438	chr1:247347971-247366380	ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Enhancers Active TSS	TF binding region Chromatin interactive region lncRNA miRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10754538	LOC729806	Cis_1M	lymphoblastoid	RTeQTL
rs10754538	VN1R5	cis	cerebellum	SCAN
rs10754538	TFB2M	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247346000-247370200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr1:247346000-247371800	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr1:247347400-247362000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:247348400-247353200	Weak transcription	Brain Germinal Matrix	brain
5	chr1:247348800-247353000	Weak transcription	HSMM	muscle
6	chr1:247348800-247353200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr1:247348800-247353600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr1:247349000-247353200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr1:247349000-247353200	Weak transcription	Stomach Smooth Muscle	stomach
10	chr1:247349400-247353000	Weak transcription	NH-A	brain
11	chr1:247349400-247353600	Weak transcription	Fetal Kidney	kidney
12	chr1:247349600-247361000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:247350000-247353400	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr1:247350200-247353200	Weak transcription	Fetal Thymus	thymus
15	chr1:247350200-247353200	Weak transcription	NHDF-Ad	bronchial
16	chr1:247350400-247353200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:247350600-247353000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr1:247351000-247353400	Weak transcription	Ovary	ovary
19	chr1:247351400-247360000	ZNF genes & repeats	Dnd41	blood
20	chr1:247351600-247353200	Weak transcription	Fetal Brain Male	brain
21	chr1:247351600-247353400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr1:247351800-247356200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
23	chr1:247351800-247357600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr1:247351800-247359400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
26	chr1:247352000-247356600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr1:247352000-247358200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
28	chr1:247352000-247359200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
29	chr1:247352000-247359400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:247352000-247368200	ZNF genes & repeats	Liver	Liver
31	chr1:247352200-247353000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr1:247352200-247353000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr1:247352200-247353200	Weak transcription	Primary hematopoietic stem cells	blood
34	chr1:247352200-247353200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr1:247352200-247353200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr1:247352200-247353200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr1:247352200-247353200	Weak transcription	Brain Angular Gyrus	brain
38	chr1:247352200-247353200	Weak transcription	Fetal Lung	lung
39	chr1:247352400-247353200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr1:247352400-247353200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:247352400-247353200	Weak transcription	Left Ventricle	heart
42	chr1:247352400-247354400	Weak transcription	Thymus	Thymus
43	chr1:247352400-247355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr1:247352400-247355800	Weak transcription	Pancreas	Pancrea
45	chr1:247352600-247353000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr1:247352600-247353200	Weak transcription	Primary monocytes fromperipheralblood	blood
47	chr1:247352600-247353200	Weak transcription	Placenta	Placenta
48	chr1:247352600-247355800	Weak transcription	Lung	lung
49	chr1:247352600-247356000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
50	chr1:247352600-247356000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell

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