Variant report

Variant	rs17097983
Chromosome Location	chr1:76504331-76504332
allele	C/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	TEAD4	chr1:76504024-76504371	H1-hESC	embryonic stem cell:	n/a	n/a
2	TEAD4	chr1:76503955-76504533	SK-N-SH	brain:	n/a	n/a
3	NFIC	chr1:76503821-76504504	SK-N-SH	brain:	n/a	n/a
4	JUND	chr1:76503856-76504503	SK-N-SH	brain:	n/a	n/a
5	FOSL2	chr1:76503839-76504387	SK-N-SH	brain:	n/a	n/a
6	JUND	chr1:76503733-76504442	SK-N-SH	brain:	n/a	n/a
7	PBX3	chr1:76503823-76504471	SK-N-SH	brain:	n/a	n/a
8	TEAD4	chr1:76503754-76504505	SK-N-SH	brain:	n/a	n/a
9	PBX3	chr1:76503941-76504358	SK-N-SH	brain:	n/a	n/a
10	TCF12	chr1:76503857-76504539	SK-N-SH	brain:	n/a	n/a
11	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
12	POLR2A	chr1:76503857-76504382	SK-N-SH	brain:	n/a	n/a
13	TCF12	chr1:76503809-76504549	SK-N-SH	brain:	n/a	n/a
14	EP300	chr1:76503721-76504518	SK-N-SH	brain:	n/a	chr1:76503992-76504006
15	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: 39 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1013630	0.91[AFR][1000 genomes]
rs10493577	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873864	0.86[EUR][1000 genomes]
rs11162069	0.86[EUR][1000 genomes]
rs11808413	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251472	0.86[ASN][1000 genomes]
rs1251493	0.85[EUR][1000 genomes]
rs1251497	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1251523	0.92[EUR][1000 genomes]
rs1251524	0.92[EUR][1000 genomes]
rs1251525	0.92[EUR][1000 genomes]
rs1251527	0.92[EUR][1000 genomes]
rs12756159	0.86[EUR][1000 genomes]
rs1340688	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1340689	0.91[AFR][1000 genomes]
rs1370715	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097922	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097929	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097968	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17097997	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1856835	0.89[AFR][1000 genomes]
rs1866254	0.86[EUR][1000 genomes]
rs1934815	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1934817	0.86[EUR][1000 genomes]
rs2118530	0.86[EUR][1000 genomes]
rs2153544	0.86[EUR][1000 genomes]
rs291074	0.86[ASN][1000 genomes]
rs3179693	0.84[EUR][1000 genomes]
rs4381138	0.89[AFR][1000 genomes]
rs58963591	0.83[ASN][1000 genomes]
rs61771293	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61771304	0.82[AFR][1000 genomes]
rs6668566	0.89[AFR][1000 genomes]
rs6672844	0.86[EUR][1000 genomes]
rs6703034	0.86[EUR][1000 genomes]
rs7533088	0.86[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	chr1:76501800-76504400	Enhancers	ES-I3 Cell Line	embryonic stem cell
2	chr1:76502200-76507200	Enhancers	Fetal Intestine Large	intestine
3	chr1:76502200-76507400	Enhancers	Fetal Intestine Small	intestine
4	chr1:76503000-76504400	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr1:76503000-76504800	Enhancers	Fetal Kidney	kidney
6	chr1:76503000-76505200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr1:76503200-76504400	Enhancers	Duodenum Mucosa	Duodenum
8	chr1:76503200-76505000	Enhancers	Placenta Amnion	Placenta Amnion
9	chr1:76503400-76505200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:76503400-76505800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr1:76503400-76505800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr1:76503400-76507000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr1:76503600-76504800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:76503600-76505800	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr1:76503600-76509600	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr1:76504000-76505000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:76504000-76505200	Enhancers	HUES64 Cell Line	embryonic stem cell
18	chr1:76504000-76509200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:76504200-76504400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr1:76504200-76504400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
21	chr1:76504200-76504600	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr1:76504200-76505800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr1:76504200-76506000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr1:76504200-76506000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr1:76504200-76506200	Weak transcription	Fetal Lung	lung
26	chr1:76504200-76506600	Weak transcription	Fetal Stomach	stomach
27	chr1:76504200-76507400	Weak transcription	HUES48 Cell Line	embryonic stem cell

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