Variant report

Variant	rs6674425
Chromosome Location	chr1:247493031-247493032
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:247492967-247493065	K562	blood:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:247237656..247243483-chr1:247491762..247497969,8	K562	blood:
2	chr1:247371907..247375145-chr1:247492885..247497524,4	MCF-7	breast:
3	chr1:247367024..247369929-chr1:247491044..247493190,2	MCF-7	breast:
4	chr1:247473800..247482682-chr1:247490121..247498423,19	K562	blood:
5	chr1:247492758..247493504-chr8:104033164..104034039,2	Hela-S3	cervix:

No data

Variant related genes	Relation type
ZNF496	TF binding region
ENSG00000254236	Chromatin interaction
ENSG00000155097	Chromatin interaction
ENSG00000162714	Chromatin interaction
ENSG00000252516	Chromatin interaction
ENSG00000227671	Chromatin interaction
ENSG00000135747	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10754542	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10754544	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10924983	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10924985	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10924989	0.86[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs11578583	0.86[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1192830	0.95[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1192831	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1192832	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12035515	0.85[ASN][1000 genomes]
rs1204493	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1616299	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1771943	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1771948	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1778544	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1778546	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1778549	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2153631	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2799540	0.80[EUR][1000 genomes]
rs3850824	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4320815	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925532	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925533	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4925534	0.86[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4925615	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs4925621	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56037169	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56399534	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6692645	0.87[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7418221	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7528202	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7540329	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7552292	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs875883	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9426180	0.90[CEU][hapmap];0.89[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9426181	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426182	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9426233	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9725334	0.87[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	esv3411043	chr1:247382851-247517729	Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
3	esv3378684	chr1:247382994-247518438	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	n/a
4	nsv833137	chr1:247437317-247607428	Flanking Active TSS Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	n/a
5	esv1848384	chr1:247485654-247495666	Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
6	nsv873439	chr1:247486736-247549220	Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	n/a
7	esv1811709	chr1:247491143-247495666	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
8	esv1840501	chr1:247491143-247495666	Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs6674425	ZNF496	cis	Esophagus Muscularis	GTEx
rs6674425	ZNF496	cis	lung	GTEx
rs6674425	ZNF496	cis	Nerve Tibial	GTEx
rs6674425	ZNF496	cis	Thyroid	GTEx

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:247456000-247493400	Weak transcription	Right Atrium	heart
2	chr1:247460400-247493400	Strong transcription	Fetal Muscle Leg	muscle
3	chr1:247460800-247493400	Strong transcription	Fetal Muscle Trunk	muscle
4	chr1:247461400-247493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:247463000-247493600	Strong transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:247463200-247493400	Strong transcription	HUES48 Cell Line	embryonic stem cell
7	chr1:247464800-247493400	Strong transcription	Fetal Stomach	stomach
8	chr1:247465200-247493400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:247467600-247493800	Weak transcription	Stomach Mucosa	stomach
10	chr1:247468400-247494000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr1:247469000-247493600	Weak transcription	Psoas Muscle	Psoas
12	chr1:247469400-247493800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr1:247471800-247493400	Weak transcription	Fetal Heart	heart
14	chr1:247472800-247493400	Weak transcription	Small Intestine	intestine
15	chr1:247476600-247494000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr1:247480000-247493600	Weak transcription	NHDF-Ad	bronchial
17	chr1:247482400-247493600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr1:247482600-247493400	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr1:247482600-247493400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr1:247482800-247493400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:247482800-247493400	Strong transcription	A549	lung
22	chr1:247482800-247493600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr1:247483000-247493200	Strong transcription	Brain Germinal Matrix	brain
24	chr1:247483000-247493200	Strong transcription	Fetal Brain Female	brain
25	chr1:247483400-247493200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
26	chr1:247484600-247493400	Weak transcription	Ovary	ovary
27	chr1:247486400-247493400	Strong transcription	NH-A	brain
28	chr1:247486800-247493400	Weak transcription	Primary B cells from cord blood	blood
29	chr1:247487000-247493400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr1:247487200-247493400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr1:247487600-247493400	Strong transcription	K562	blood
32	chr1:247488200-247493400	Strong transcription	Brain Hippocampus Middle	brain
33	chr1:247488200-247493600	Strong transcription	Osteobl	bone
34	chr1:247488600-247493200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr1:247488600-247493200	Strong transcription	Left Ventricle	heart
36	chr1:247488600-247493400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:247488600-247493400	Strong transcription	Fetal Intestine Small	intestine
38	chr1:247488600-247493600	Strong transcription	H9 Cell Line	embryonic stem cell
39	chr1:247488800-247493400	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr1:247489000-247493400	Strong transcription	HUES64 Cell Line	embryonic stem cell
41	chr1:247489000-247493400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr1:247489000-247493400	Strong transcription	Fetal Intestine Large	intestine
43	chr1:247489000-247493400	Strong transcription	NHEK	skin
44	chr1:247489200-247493200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:247489200-247493200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:247489400-247493200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
47	chr1:247489400-247493400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:247489600-247493200	Strong transcription	Brain Substantia Nigra	brain
49	chr1:247489600-247493400	Strong transcription	Placenta	Placenta
50	chr1:247489800-247493200	Strong transcription	Colon Smooth Muscle	Colon

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