Variant report

Variant	rs2187562
Chromosome Location	chr1:174811651-174811652
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174810056..174811969-chr1:174966210..174968359,2	K562	blood:

Variant related genes	Relation type
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs10436863	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1046439	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs11804941	0.81[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs12060177	0.81[AFR][1000 genomes]
rs12083837	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1653626	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1653627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1653632	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs170768	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap]
rs1754349	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1754351	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs1754355	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1793297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1793300	0.89[EUR][1000 genomes]
rs1793309	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1793319	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap]
rs1801791	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs1984418	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs2105949	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs2285210	0.91[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap]
rs2981894	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2987869	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2987874	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3018410	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3118980	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[MKK][hapmap];0.87[TSI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3133270	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs332765	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];0.83[EUR][1000 genomes]
rs332770	0.86[EUR][1000 genomes]
rs332771	0.86[EUR][1000 genomes]
rs332773	0.87[EUR][1000 genomes]
rs332783	0.83[CEU][hapmap]
rs332789	0.86[EUR][1000 genomes]
rs332791	0.85[EUR][1000 genomes]
rs332795	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.93[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs332796	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap]
rs332805	0.82[EUR][1000 genomes]
rs333418	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap]
rs34819375	0.82[EUR][1000 genomes]
rs3753563	1.00[CHB][hapmap];0.83[CHD][hapmap];0.91[JPT][hapmap]
rs4233195	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs444678	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs461910	0.86[EUR][1000 genomes]
rs4650666	0.80[CEU][hapmap]
rs4651238	0.84[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs55741955	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828140	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61828142	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6425305	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6425309	0.81[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap]
rs6425310	0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap]
rs6656665	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6658861	0.86[ASW][hapmap];0.84[CEU][hapmap];0.81[GIH][hapmap];0.82[LWK][hapmap];0.83[MEX][hapmap]
rs6665216	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6669560	0.91[CHB][hapmap];0.83[CHD][hapmap]
rs66700013	0.82[EUR][1000 genomes]
rs6683602	0.81[AFR][1000 genomes]
rs6688577	0.80[CEU][hapmap];0.81[GIH][hapmap]
rs6696197	0.81[AFR][1000 genomes]
rs6701968	1.00[YRI][hapmap]
rs67967476	0.81[AFR][1000 genomes]
rs7538588	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7545910	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9700904	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9804056	0.84[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs989423	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
4	esv1844208	chr1:174764839-174818547	Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	esv1847553	chr1:174764839-174818547	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv1815488	chr1:174794144-174818547	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv1821003	chr1:174794144-174818547	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
8	esv1844568	chr1:174794144-174818547	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv872556	chr1:174794420-174819336	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	esv1844237	chr1:174796670-174818547	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv548217	chr1:174797867-174812326	Enhancers Weak transcription Strong transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv872557	chr1:174800121-174819336	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	nsv872558	chr1:174802731-174818547	Enhancers Flanking Active TSS Active TSS Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv872559	chr1:174803606-174819336	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	nsv946510	chr1:174811249-174819547	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2187562	SLC9A11	cis	parietal	SCAN
rs2187562	MRPS14	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174782200-174813000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
2	chr1:174796600-174833400	Weak transcription	Primary B cells from cord blood	blood
3	chr1:174808200-174812200	Enhancers	HSMM	muscle
4	chr1:174810800-174811800	Enhancers	GM12878-XiMat	blood
5	chr1:174810800-174812000	Enhancers	HSMMtube	muscle
6	chr1:174811000-174812000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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