Variant report

Variant	rs6678604
Chromosome Location	chr1:247354581-247354582
allele	A/C
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	ZNF274	chr1:247352631-247354807	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:247353227..247354818-chr1:247357854..247360408,2	K562	blood:
2	chr1:247346230..247348838-chr1:247353160..247354871,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259865	TF binding region
ENSG00000215795	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10754538	0.99[ASN][1000 genomes]
rs10754539	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10802475	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10924944	0.93[ASN][1000 genomes]
rs10924949	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10924950	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10924951	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924952	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924953	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924954	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10924955	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10924957	0.96[ASN][1000 genomes]
rs10924958	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10924960	0.98[ASN][1000 genomes]
rs10924961	0.94[ASN][1000 genomes]
rs1115201	0.98[ASN][1000 genomes]
rs1132779	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12025262	0.99[ASN][1000 genomes]
rs12069092	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12071728	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12089377	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12118895	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12122649	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12131404	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133602	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133699	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12133802	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2068050	0.96[ASN][1000 genomes]
rs2380118	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3738444	0.95[ASN][1000 genomes]
rs3820509	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs4925594	0.99[ASN][1000 genomes]
rs6426226	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6426227	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6656142	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656343	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6660243	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6670847	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6676905	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6687710	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6704274	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
rs6678604	MIR3916	cis	Skin Sun Exposed Lower leg	GTEx
rs6678604	LOC729806	Cis_1M	lymphoblastoid	RTeQTL
rs6678604	MIR3916	cis	Whole Blood	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

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	chr1:247349600-247361000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr1:247351400-247360000	ZNF genes & repeats	Dnd41	blood
6	chr1:247351800-247356200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
7	chr1:247351800-247357600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
8	chr1:247351800-247359400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:247351800-247372400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
10	chr1:247352000-247356600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:247352000-247358200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr1:247352000-247359200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
13	chr1:247352000-247359400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr1:247352000-247368200	ZNF genes & repeats	Liver	Liver
15	chr1:247352400-247355800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:247352400-247355800	Weak transcription	Pancreas	Pancrea
17	chr1:247352600-247355800	Weak transcription	Lung	lung
18	chr1:247352600-247356000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
19	chr1:247352600-247356000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr1:247352600-247358200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:247352800-247356000	ZNF genes & repeats	Primary T killer memory cells from peripheral blood	blood
22	chr1:247353000-247355000	ZNF genes & repeats	HSMMtube	muscle
23	chr1:247353000-247355600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:247353000-247355800	ZNF genes & repeats	Primary T cells from cord blood	blood
25	chr1:247353000-247356000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
26	chr1:247353000-247356000	ZNF genes & repeats	Muscle Satellite Cultured Cells	--
27	chr1:247353000-247356000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:247353000-247356000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
29	chr1:247353000-247356000	ZNF genes & repeats	HSMM	muscle
30	chr1:247353000-247356200	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
31	chr1:247353000-247356600	ZNF genes & repeats	NH-A	brain
32	chr1:247353000-247357600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
33	chr1:247353000-247357800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
34	chr1:247353000-247361800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
35	chr1:247353000-247362200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr1:247353000-247367200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr1:247353000-247368000	ZNF genes & repeats	Primary B cells from cord blood	blood
38	chr1:247353000-247370400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr1:247353200-247354600	Strong transcription	Brain Germinal Matrix	brain
40	chr1:247353200-247354800	ZNF genes & repeats	Fetal Heart	heart
41	chr1:247353200-247354800	ZNF genes & repeats	Right Ventricle	heart
42	chr1:247353200-247354800	ZNF genes & repeats	NHEK	skin
43	chr1:247353200-247355000	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
44	chr1:247353200-247355000	ZNF genes & repeats	Brain Hippocampus Middle	brain
45	chr1:247353200-247355600	Strong transcription	Primary monocytes fromperipheralblood	blood
46	chr1:247353200-247356000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
47	chr1:247353200-247356000	ZNF genes & repeats	Primary T helper naive cells from peripheral blood	blood
48	chr1:247353200-247356000	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr1:247353200-247356000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:247353200-247356000	Strong transcription	Fetal Brain Male	brain

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