Variant report

Variant	rs2999545
Chromosome Location	chr1:151904146-151904147
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151902230..151904695-chr1:151916029..151918681,2	K562	blood:
2	chr1:151903606..151908213-chr1:151959560..151963672,4	MCF-7	breast:
3	chr1:151881521..151883503-chr1:151901911..151904684,3	MCF-7	breast:
4	chr1:151903334..151906140-chr1:151909030..151911005,2	K562	blood:
5	chr1:151896649..151898328-chr1:151903426..151905406,2	K562	blood:
6	chr1:151902428..151904789-chr1:152007521..152010328,2	K562	blood:

Variant related genes	Relation type
ENSG00000159445	Chromatin interaction
ENSG00000163191	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1038747	0.84[ASN][1000 genomes]
rs1060870	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10788817	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10788818	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10788820	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10888445	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11204914	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11204915	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11589720	0.88[ASN][1000 genomes]
rs12067594	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12116923	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12562586	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13320	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1387833	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1490189	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1907040	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2130525	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2279501	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2279502	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2337689	0.80[ASN][1000 genomes]
rs2338201	0.89[EUR][1000 genomes]
rs2338209	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932565	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2932576	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932577	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932579	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2932581	0.86[ASN][1000 genomes]
rs2932583	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2932586	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2999506	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2999508	0.86[ASN][1000 genomes]
rs2999512	0.86[ASN][1000 genomes]
rs2999541	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2999542	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2999544	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2999546	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007670	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007685	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3007691	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3007711	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845409	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4845713	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6685187	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6698740	0.92[EUR][1000 genomes]
rs7523082	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7541453	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7542137	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9435963	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9435964	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9943281	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][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	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547852	chr1:151843044-151955230	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv872441	chr1:151850072-152034430	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	191 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2999545	THEM4	cis	Nerve Tibial	GTEx
rs2999545	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999545	THEM4	cis	multi-tissue	Pritchard
rs2999545	THEM4	cis	Esophagus Muscularis	GTEx
rs2999545	S100A10	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151899400-151906400	Weak transcription	Fetal Intestine Small	intestine
2	chr1:151902200-151907600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151902600-151906400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:151902800-151906800	Weak transcription	Primary B cells from peripheral blood	blood

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