Variant report

Variant	rs2999542
Chromosome Location	chr1:151899559-151899560
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:151897183..151899597-chr1:151964154..151966740,2	MCF-7	breast:
2	chr1:151898614..151900829-chr1:151904276..151907229,3	K562	blood:
3	chr1:151882722..151885720-chr1:151898176..151900104,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs1038747	0.83[CHB][hapmap];0.83[JPT][hapmap];0.81[AMR][1000 genomes]
rs10494270	0.90[CHB][hapmap];0.81[TSI][hapmap]
rs1060870	0.85[AMR][1000 genomes]
rs10788817	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10788818	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10788820	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10888445	0.82[CHB][hapmap]
rs11204914	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204915	1.00[CHB][hapmap];0.84[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204922	0.81[JPT][hapmap]
rs11589720	0.81[ASN][1000 genomes]
rs12067594	0.87[AMR][1000 genomes]
rs12116923	0.86[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs12562586	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13320	0.83[CHB][hapmap];0.93[GIH][hapmap];0.90[MEX][hapmap];0.84[TSI][hapmap]
rs1387833	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1490189	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16833668	0.86[CHB][hapmap]
rs16833728	0.81[CHB][hapmap]
rs1907040	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2130525	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279501	0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2279502	0.91[CHB][hapmap];0.87[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2338019	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs2338201	0.83[AMR][1000 genomes]
rs2338209	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932565	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2932576	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932577	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932579	0.96[CEU][hapmap];0.95[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2932581	0.80[AMR][1000 genomes]
rs2932583	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2932586	0.82[ASN][1000 genomes]
rs2932590	0.86[CHB][hapmap];0.81[JPT][hapmap];0.86[TSI][hapmap]
rs2999506	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2999508	0.80[AMR][1000 genomes]
rs2999526	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap];0.84[TSI][hapmap]
rs2999528	0.86[CHB][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap]
rs2999531	0.81[CHB][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs2999541	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999544	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2999545	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2999546	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3007670	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007685	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3007691	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs3007708	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs3007711	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845409	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4845713	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587635	0.81[CHB][hapmap]
rs6587636	0.81[CHB][hapmap]
rs6662611	0.81[CHB][hapmap]
rs6663064	0.86[CHB][hapmap]
rs6685187	0.83[CHB][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.84[TSI][hapmap];0.83[AMR][1000 genomes]
rs6686874	0.86[CHB][hapmap]
rs6698740	0.85[AMR][1000 genomes]
rs6703465	0.81[CHB][hapmap]
rs7523082	0.81[CHB][hapmap]
rs7535002	0.86[CHB][hapmap]
rs7541099	0.81[CHB][hapmap]
rs7542137	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs902313	0.81[CHB][hapmap]
rs9435963	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9435964	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs971887	0.81[CHB][hapmap]
rs9943221	0.91[CHB][hapmap];0.81[GIH][hapmap]
rs9943251	0.87[CHB][hapmap]
rs9943281	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2999542	THEM4	cis	parietal	SCAN
rs2999542	THEM4	cis	Nerve Tibial	GTEx
rs2999542	THEM4	cis	multi-tissue	Pritchard
rs2999542	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999542	S100A10	cis	cerebellum	SCAN
rs2999542	THEM4	cis	cerebellum	SCAN
rs2999542	THEM4	cis	lymphoblastoid	seeQTL
rs2999542	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2999542	S100A10	cis	multi-tissue	Pritchard
rs2999542	THEM4	cis	Esophagus Muscularis	GTEx
rs2999542	S100A10	cis	lymphoblastoid	seeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151898200-151900600	Enhancers	GM12878-XiMat	blood
2	chr1:151898200-151902600	Weak transcription	Primary B cells from peripheral blood	blood
3	chr1:151898400-151899600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr1:151899400-151899600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:151899400-151906400	Weak transcription	Fetal Intestine Small	intestine

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