Variant report

Variant	rs1340689
Chromosome Location	chr1:76506409-76506410
allele	A/T
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	KAP1	chr1:76505822-76506601	HEK293	kidney:	n/a	n/a
2	KAP1	chr1:76505681-76506613	U2OS	brain:	n/a	n/a
3	GATA1	chr1:76506064-76506422	PBDEFetal	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000230027	TF binding region

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1013629	0.94[EUR][1000 genomes]
rs1013630	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10430051	0.84[EUR][1000 genomes]
rs10493579	0.81[ASN][1000 genomes]
rs11162071	0.81[ASN][1000 genomes]
rs11162072	0.81[ASN][1000 genomes]
rs11808413	0.86[AFR][1000 genomes]
rs1251490	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12753569	0.84[EUR][1000 genomes]
rs1370715	0.87[AFR][1000 genomes]
rs17097922	0.84[AFR][1000 genomes]
rs17097968	0.89[AFR][1000 genomes]
rs17097983	0.91[AFR][1000 genomes]
rs17097997	0.91[AFR][1000 genomes]
rs17606806	0.81[ASN][1000 genomes]
rs1856835	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35821217	0.81[ASN][1000 genomes]
rs4381138	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4576618	0.81[ASN][1000 genomes]
rs61771304	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6593523	0.84[EUR][1000 genomes]
rs6668566	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669349	0.81[ASN][1000 genomes]
rs6676370	0.84[EUR][1000 genomes]
rs6696116	0.84[EUR][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	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
2	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
3	chr1:76503400-76507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:76503600-76509600	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr1:76504000-76509200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr1:76504200-76506600	Weak transcription	Fetal Stomach	stomach
7	chr1:76504200-76507400	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr1:76505600-76506600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
9	chr1:76505600-76506600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:76505600-76507400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr1:76505800-76506600	Enhancers	HUES6 Cell Line	embryonic stem cell
12	chr1:76505800-76506800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:76505800-76506800	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:76505800-76507000	Enhancers	iPS-18 Cell Line	embryonic stem cell
15	chr1:76505800-76507200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:76505800-76507800	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr1:76506000-76506800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr1:76506000-76506800	Enhancers	HUES64 Cell Line	embryonic stem cell
19	chr1:76506000-76506800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:76506000-76507800	Enhancers	Placenta Amnion	Placenta Amnion
21	chr1:76506200-76506600	Enhancers	Fetal Lung	lung
22	chr1:76506200-76506600	Enhancers	Rectal Mucosa Donor 29	rectum
23	chr1:76506200-76507400	Enhancers	ES-I3 Cell Line	embryonic stem cell
24	chr1:76506200-76507400	Enhancers	Rectal Mucosa Donor 31	rectum
25	chr1:76506200-76508000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:76506400-76506600	Enhancers	Fetal Heart	heart
27	chr1:76506400-76514000	Weak transcription	H1 Cell Line	embryonic stem cell

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