Variant report

Variant	rs6692421
Chromosome Location	chr1:76503776-76503777
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	JUND	chr1:76503733-76504442	SK-N-SH	brain:	n/a	n/a
2	TEAD4	chr1:76503754-76504505	SK-N-SH	brain:	n/a	n/a
3	GATA3	chr1:76503688-76504539	SK-N-SH	brain:	n/a	chr1:76504068-76504077 chr1:76504066-76504079 chr1:76504066-76504078 chr1:76504068-76504075 chr1:76504064-76504080 chr1:76504067-76504077
4	EP300	chr1:76503721-76504518	SK-N-SH	brain:	n/a	chr1:76503992-76504006
5	GATA3	chr1:76503581-76504588	SK-N-SH	brain:	n/a	chr1:76504068-76504077 chr1:76504066-76504079 chr1:76504066-76504078 chr1:76504068-76504075 chr1:76504064-76504080 chr1:76504067-76504077

Variant related genes	Relation type
ENSG00000230027	TF binding region

Extended variants
information (count: 42 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10493580	0.90[ASN][1000 genomes]
rs10873865	0.87[AFR][1000 genomes]
rs11162070	0.90[ASN][1000 genomes]
rs11162073	0.88[ASN][1000 genomes]
rs11804459	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11805321	0.90[ASN][1000 genomes]
rs12032833	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12032853	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12033420	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038667	0.90[ASN][1000 genomes]
rs12039427	0.90[ASN][1000 genomes]
rs12040748	0.90[ASN][1000 genomes]
rs12040836	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1344929	0.96[EUR][1000 genomes]
rs1370714	0.98[AFR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17599859	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1934816	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4083965	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4146895	0.82[ASN][1000 genomes]
rs4146896	0.82[ASN][1000 genomes]
rs4949690	0.90[ASN][1000 genomes]
rs5022490	0.87[AFR][1000 genomes]
rs59862803	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61771303	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6679705	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6685661	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6686341	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688109	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6688802	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6696470	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703050	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703053	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6703146	0.90[ASN][1000 genomes]
rs7513692	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7517793	0.90[ASN][1000 genomes]
rs7517974	0.90[ASN][1000 genomes]
rs7529565	0.90[ASN][1000 genomes]
rs7536325	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7550814	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	esv2754129	chr1:76489579-76529279	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76501800-76504200	Enhancers	iPS-20b Cell Line	embryonic stem cell
2	chr1:76501800-76504400	Enhancers	ES-I3 Cell Line	embryonic stem cell
3	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
4	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
5	chr1:76502600-76503800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr1:76502800-76504000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr1:76502800-76504200	Enhancers	Stomach Mucosa	stomach
8	chr1:76503000-76503800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
9	chr1:76503000-76504200	Enhancers	Fetal Stomach	stomach
10	chr1:76503000-76504400	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr1:76503000-76504800	Enhancers	Fetal Kidney	kidney
12	chr1:76503000-76505200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr1:76503200-76504000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr1:76503200-76504200	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:76503200-76504200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr1:76503200-76504400	Enhancers	Duodenum Mucosa	Duodenum
17	chr1:76503200-76505000	Enhancers	Placenta Amnion	Placenta Amnion
18	chr1:76503400-76504200	Enhancers	Fetal Lung	lung
19	chr1:76503400-76505200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr1:76503400-76505800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
21	chr1:76503400-76505800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr1:76503400-76507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:76503600-76504000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr1:76503600-76504200	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:76503600-76504800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:76503600-76505800	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr1:76503600-76509600	Weak transcription	Sigmoid Colon	Sigmoid Colon

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