Variant report

Variant	rs3762268
Chromosome Location	chr1:153522350-153522351
allele	A/G
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	BCL3	chr1:153521554-153522378	A549	lung:	n/a	chr1:153521900-153521909 chr1:153521816-153521825
2	FOSL2	chr1:153521378-153522629	A549	lung:	n/a	chr1:153521951-153521961 chr1:153522535-153522543 chr1:153521951-153521961 chr1:153521951-153521961
3	MAX	chr1:153521272-153522372	A549	lung:	n/a	n/a
4	FOXA2	chr1:153521416-153522380	A549	lung:	n/a	n/a
5	NFIC	chr1:153521569-153522354	SK-N-SH	brain:	n/a	n/a
6	GATA3	chr1:153521216-153522404	A549	lung:	n/a	chr1:153521953-153521962
7	CTCF	chr1:153522220-153522370	HVMF	connective:	n/a	n/a
8	TCF12	chr1:153521432-153522366	SK-N-SH	brain:	n/a	n/a
9	CTCF	chr1:153522220-153522370	WERI-Rb-1	eye:	n/a	n/a
10	TCF12	chr1:153521646-153522358	ECC-1	luminal epithelium:	n/a	n/a
11	JUND	chr1:153521559-153522359	SK-N-SH	brain:	n/a	chr1:153521951-153521961 chr1:153521951-153521961 chr1:153521951-153521961
12	MAX	chr1:153519483-153522520	A549	lung:	n/a	chr1:153520680-153520690
13	JUND	chr1:153521583-153522460	SK-N-SH	brain:	n/a	chr1:153521951-153521961 chr1:153521951-153521961 chr1:153521951-153521961
14	EP300	chr1:153521566-153522358	SK-N-SH	brain:	n/a	chr1:153521987-153522003
15	POLR2A	chr1:153521989-153522472	K562	blood:	n/a	n/a
16	MAZ	chr1:153520977-153522850	IMR90	lung:	n/a	n/a
17	POLR2A	chr1:153517452-153526571	MCF10A-Er-Src	breast:	n/a	n/a
18	TCF12	chr1:153521126-153522523	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153508236..153509740-chr1:153522237..153524623,2	K562	blood:
2	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
3	chr1:153522267..153525133-chr1:153537337..153540137,3	MCF-7	breast:
4	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
5	chr1:153504382..153507280-chr1:153522086..153523762,2	K562	blood:

Variant related genes	Relation type
S100A4	TF binding region
S100A3	TF binding region
ENSG00000196754	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000238279	Chromatin interaction
ENSG00000189334	Chromatin interaction
ENSG00000197956	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1047325	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs1050923	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.83[TSI][hapmap];0.94[EUR][1000 genomes]
rs11488669	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs16835437	1.00[CEU][hapmap];0.90[GIH][hapmap];0.83[TSI][hapmap];0.91[EUR][1000 genomes]
rs16835455	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs1810765	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs28452456	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28548347	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28594230	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28689606	0.97[EUR][1000 genomes]
rs28718953	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36022742	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs41265162	0.94[EUR][1000 genomes]
rs41265164	0.94[EUR][1000 genomes]
rs4595398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.96[YRI][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55955983	1.00[EUR][1000 genomes]
rs56043239	0.94[EUR][1000 genomes]
rs56057245	0.84[EUR][1000 genomes]
rs56089062	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56350425	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56838169	0.94[EUR][1000 genomes]
rs57024596	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59376279	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60218214	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60287468	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60969679	0.81[EUR][1000 genomes]
rs61265945	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61558997	0.91[EUR][1000 genomes]
rs6427301	1.00[EUR][1000 genomes]
rs6671398	0.94[EUR][1000 genomes]
rs6700310	0.91[EUR][1000 genomes]
rs6702891	0.90[GIH][hapmap]
rs6703014	0.90[GIH][hapmap]
rs73026350	0.94[EUR][1000 genomes]
rs74115473	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74115476	0.97[EUR][1000 genomes]
rs743687	0.82[EUR][1000 genomes]
rs7535476	0.84[EUR][1000 genomes]
rs8401	1.00[CEU][hapmap];0.90[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs9427239	0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010488	chr1:152901263-153670972	Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
2	nsv535171	chr1:152901263-153670972	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	236 gene(s)	inside rSNPs	diseases
3	nsv1002705	chr1:153307852-153525589	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	nsv831603	chr1:153405842-153576143	Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	148 gene(s)	inside rSNPs	diseases
5	nsv1007306	chr1:153413827-153541798	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	146 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153509400-153527600	Enhancers	Breast Myoepithelial Primary Cells	Breast
2	chr1:153512400-153522400	Enhancers	Stomach Mucosa	stomach
3	chr1:153515400-153522800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:153515400-153523000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr1:153516800-153522400	Enhancers	Fetal Intestine Small	intestine
6	chr1:153517200-153522400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:153517400-153524000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:153517600-153522800	Enhancers	Spleen	Spleen
9	chr1:153518000-153522600	Enhancers	Fetal Stomach	stomach
10	chr1:153518200-153523000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:153518200-153524000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr1:153518200-153524000	Enhancers	K562	blood
13	chr1:153518400-153522800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr1:153518400-153523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr1:153518600-153522400	Weak transcription	Fetal Lung	lung
16	chr1:153518600-153522400	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr1:153518600-153522800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr1:153518600-153523600	Enhancers	Fetal Thymus	thymus
19	chr1:153518600-153524000	Enhancers	HUES6 Cell Line	embryonic stem cell
20	chr1:153518600-153524000	Enhancers	Placenta	Placenta
21	chr1:153518600-153524200	Enhancers	Lung	lung
22	chr1:153518800-153523200	Enhancers	Right Atrium	heart
23	chr1:153518800-153524200	Enhancers	Esophagus	oesophagus
24	chr1:153519000-153522800	Enhancers	Duodenum Smooth Muscle	Duodenum
25	chr1:153519000-153524400	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr1:153519200-153522400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr1:153519200-153523400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr1:153519200-153524000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr1:153519200-153524200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:153519200-153524400	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr1:153519400-153522800	Enhancers	NHLF	lung
32	chr1:153519400-153523400	Enhancers	Placenta Amnion	Placenta Amnion
33	chr1:153519400-153523600	Enhancers	Fetal Muscle Leg	muscle
34	chr1:153519400-153526000	Weak transcription	Aorta	Aorta
35	chr1:153519600-153522400	Enhancers	Rectal Smooth Muscle	rectum
36	chr1:153519600-153523000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:153519800-153523600	Enhancers	Fetal Muscle Trunk	muscle
38	chr1:153520000-153523600	Enhancers	Skeletal Muscle Male	skeletal muscle
39	chr1:153520000-153529400	Genic enhancers	HMEC	breast
40	chr1:153520200-153524200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
41	chr1:153520400-153522600	Weak transcription	Primary hematopoietic stem cells	blood
42	chr1:153520400-153524200	Enhancers	Adipose Nuclei	Adipose
43	chr1:153520600-153522400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr1:153520600-153522600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr1:153520800-153522600	Enhancers	Colonic Mucosa	Colon
46	chr1:153520800-153522800	Enhancers	Right Ventricle	heart
47	chr1:153520800-153523200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr1:153520800-153523200	Enhancers	Left Ventricle	heart
49	chr1:153521000-153522400	Flanking Active TSS	A549	lung
50	chr1:153521000-153522600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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