Variant report

Variant	rs57024596
Chromosome Location	chr1:153521496-153521497
allele	C/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	EP300	chr1:153521245-153522249	A549	lung:	n/a	chr1:153521987-153522003
2	FOSL2	chr1:153521378-153522629	A549	lung:	n/a	chr1:153521951-153521961 chr1:153522535-153522543 chr1:153521951-153521961 chr1:153521951-153521961
3	EP300	chr1:153521414-153522177	A549	lung:	n/a	chr1:153521987-153522003
4	MAX	chr1:153521272-153522372	A549	lung:	n/a	n/a
5	FOXA2	chr1:153521416-153522380	A549	lung:	n/a	n/a
6	GATA3	chr1:153521216-153522404	A549	lung:	n/a	chr1:153521953-153521962
7	TCF12	chr1:153521432-153522366	SK-N-SH	brain:	n/a	n/a
8	SIX5	chr1:153521402-153522286	A549	lung:	n/a	n/a
9	MAX	chr1:153519483-153522520	A549	lung:	n/a	chr1:153520680-153520690
10	MAZ	chr1:153520977-153522850	IMR90	lung:	n/a	n/a
11	POLR2A	chr1:153517452-153526571	MCF10A-Er-Src	breast:	n/a	n/a
12	REST	chr1:153521311-153522304	A549	lung:	n/a	n/a
13	TCF12	chr1:153521126-153522523	A549	lung:	n/a	n/a
14	SP1	chr1:153521234-153522330	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:153519598..153522352-chr1:153580214..153582486,2	K562	blood:
2	chr1:153518882..153521795-chr1:153587475..153590405,3	MCF-7	breast:
3	chr1:153514095..153517799-chr1:153518495..153521571,4	K562	blood:
4	chr1:153519212..153523090-chr1:153584863..153588698,4	MCF-7	breast:
5	chr1:153515310..153522123-chr1:153537390..153541283,13	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-S100A1-1	chr1:153520897-153521591	ENSG00000247613

Variant related genes	Relation type
S100A4	TF binding region
ENSG00000196420	Chromatin interaction
ENSG00000188643	Chromatin interaction
ENSG00000196754	Chromatin interaction
ENSG00000196154	Chromatin interaction
ENSG00000189334	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1047325	0.91[EUR][1000 genomes]
rs1050923	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11488669	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16835437	0.91[EUR][1000 genomes]
rs16835455	0.91[EUR][1000 genomes]
rs1810765	0.82[EUR][1000 genomes]
rs28452456	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28548347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28594230	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28689606	0.97[EUR][1000 genomes]
rs28718953	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36022742	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3762268	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41265160	0.80[AFR][1000 genomes]
rs41265162	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41265164	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4595398	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55955983	0.94[EUR][1000 genomes]
rs56043239	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56057245	0.84[EUR][1000 genomes]
rs56089062	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56350425	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56838169	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58056804	0.97[EUR][1000 genomes]
rs58072118	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59376279	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60218214	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60287468	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60969679	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs61265945	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61558997	0.91[EUR][1000 genomes]
rs6427301	0.94[EUR][1000 genomes]
rs6671398	0.88[EUR][1000 genomes]
rs6700310	0.91[EUR][1000 genomes]
rs73026350	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs74115473	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs74115476	0.91[EUR][1000 genomes]
rs743687	0.82[EUR][1000 genomes]
rs7535476	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8401	0.88[EUR][1000 genomes]

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:100 , 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	chr1:153516800-153521800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:153516800-153522000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:153516800-153522400	Enhancers	Fetal Intestine Small	intestine
8	chr1:153517200-153522400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:153517400-153524000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr1:153517600-153522800	Enhancers	Spleen	Spleen
11	chr1:153518000-153522600	Enhancers	Fetal Stomach	stomach
12	chr1:153518200-153521800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr1:153518200-153521800	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr1:153518200-153523000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr1:153518200-153524000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr1:153518200-153524000	Enhancers	K562	blood
17	chr1:153518400-153522200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr1:153518400-153522800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr1:153518400-153523800	Enhancers	ES-I3 Cell Line	embryonic stem cell
20	chr1:153518600-153521600	Weak transcription	GM12878-XiMat	blood
21	chr1:153518600-153521800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr1:153518600-153522000	Weak transcription	Gastric	stomach
23	chr1:153518600-153522400	Weak transcription	Fetal Lung	lung
24	chr1:153518600-153522400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:153518600-153522800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr1:153518600-153523600	Enhancers	Fetal Thymus	thymus
27	chr1:153518600-153524000	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr1:153518600-153524000	Enhancers	Placenta	Placenta
29	chr1:153518600-153524200	Enhancers	Lung	lung
30	chr1:153518800-153521600	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr1:153518800-153523200	Enhancers	Right Atrium	heart
32	chr1:153518800-153524200	Enhancers	Esophagus	oesophagus
33	chr1:153519000-153522800	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr1:153519000-153524400	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr1:153519200-153522000	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr1:153519200-153522000	Enhancers	Primary neutrophils fromperipheralblood	blood
37	chr1:153519200-153522400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr1:153519200-153523400	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr1:153519200-153524000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr1:153519200-153524200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr1:153519200-153524400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr1:153519400-153522800	Enhancers	NHLF	lung
43	chr1:153519400-153523400	Enhancers	Placenta Amnion	Placenta Amnion
44	chr1:153519400-153523600	Enhancers	Fetal Muscle Leg	muscle
45	chr1:153519400-153526000	Weak transcription	Aorta	Aorta
46	chr1:153519600-153522000	Enhancers	H1 Cell Line	embryonic stem cell
47	chr1:153519600-153522400	Enhancers	Rectal Smooth Muscle	rectum
48	chr1:153519600-153523000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr1:153519800-153521600	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:153519800-153523600	Enhancers	Fetal Muscle Trunk	muscle

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