Variant report

Variant	rs4521985
Chromosome Location	chr1:154123523-154123524
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153962510..153964616-chr1:154122423..154124331,2	MCF-7	breast:
2	chr1:154121564..154123790-chr1:154128887..154131552,2	K562	blood:
3	chr1:154122896..154125457-chr1:154127729..154131254,3	MCF-7	breast:
4	chr1:154121866..154123799-chr1:154125577..154127582,4	K562	blood:

Variant related genes	Relation type
ENSG00000177954	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1051370	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10797067	0.81[CHB][hapmap]
rs10908558	0.95[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs10908627	0.91[ASW][hapmap]
rs10908723	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11264680	0.83[ASW][hapmap];0.82[LWK][hapmap];0.83[MKK][hapmap];0.89[YRI][hapmap]
rs11264743	0.95[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs11264866	0.91[ASW][hapmap]
rs11264871	0.90[YRI][hapmap]
rs11264873	0.82[YRI][hapmap]
rs11264875	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs11264886	0.82[YRI][hapmap]
rs11264964	0.83[ASW][hapmap];1.00[YRI][hapmap]
rs11264974	0.82[YRI][hapmap]
rs11265049	1.00[YRI][hapmap]
rs11265076	1.00[YRI][hapmap]
rs11265082	0.91[ASW][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap]
rs11265099	0.95[LWK][hapmap];0.83[MKK][hapmap]
rs11265122	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265299	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs12021641	0.91[ASW][hapmap];0.87[LWK][hapmap];0.80[MKK][hapmap];0.90[YRI][hapmap]
rs12026475	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.81[ASN][1000 genomes]
rs12048137	0.82[YRI][hapmap]
rs1212352	0.82[CHB][hapmap];0.91[CHD][hapmap];0.86[JPT][hapmap]
rs12405309	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs12408170	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12408458	0.91[CHB][hapmap];0.93[CHD][hapmap];0.86[JPT][hapmap];0.85[MKK][hapmap]
rs12564669	0.88[YRI][hapmap]
rs12568280	0.82[EUR][1000 genomes]
rs3196889	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3791187	0.82[LWK][hapmap];0.80[MKK][hapmap];0.89[YRI][hapmap]
rs3828076	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs4845363	1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845597	1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap]
rs4845600	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845601	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55677228	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60633748	0.83[EUR][1000 genomes]
rs6659053	1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.82[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6664278	0.92[CEU][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.80[YRI][hapmap]
rs6667928	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671166	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6672856	0.83[ASW][hapmap]
rs6673171	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6678826	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs6693620	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6701341	0.91[ASW][hapmap]
rs72696227	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7517127	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7521303	1.00[YRI][hapmap]
rs7535778	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7547663	1.00[YRI][hapmap]
rs7552737	0.91[ASW][hapmap];0.91[LWK][hapmap];0.86[MKK][hapmap];0.90[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases
4	esv1830240	chr1:153885261-154370938	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	239 gene(s)	inside rSNPs	diseases
5	nsv948413	chr1:153974621-154797272	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	132 gene(s)	inside rSNPs	diseases
6	nsv1000402	chr1:153991106-154527053	Strong transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
7	nsv520398	chr1:154068196-154141908	Strong transcription Flanking Active TSS Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
8	nsv1000153	chr1:154074249-154152417	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
9	nsv872451	chr1:154101519-154139757	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs4521985	FLG	cis	parietal	SCAN
rs4521985	SPRR2D	cis	parietal	SCAN
rs4521985	SCARNA4	cis	cerebellum	SCAN
rs4521985	SLC27A3	cis	cerebellum	SCAN
rs4521985	RAB13	cis	lymphoblastoid	seeQTL
rs4521985	UBAP2L	cis	multi-tissue	Pritchard

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154112200-154138400	Weak transcription	Psoas Muscle	Psoas
2	chr1:154114600-154126800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
3	chr1:154119600-154127000	Weak transcription	Esophagus	oesophagus
4	chr1:154120200-154123600	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr1:154121000-154125200	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr1:154121000-154127000	Weak transcription	Pancreas	Pancrea
7	chr1:154121400-154127000	Weak transcription	A549	lung
8	chr1:154121600-154123800	Weak transcription	HUVEC	blood vessel
9	chr1:154121600-154125200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:154121600-154126200	Weak transcription	K562	blood
11	chr1:154121600-154126600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:154121800-154124000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:154121800-154126400	Weak transcription	Spleen	Spleen
14	chr1:154122000-154126200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr1:154122000-154126200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr1:154122000-154126800	Weak transcription	GM12878-XiMat	blood
17	chr1:154122200-154125800	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr1:154122200-154126000	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr1:154122200-154126400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr1:154122200-154126400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:154122200-154127000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr1:154122600-154126200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr1:154122600-154126400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:154123400-154124400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:154123400-154124400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr1:154123400-154124400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr1:154123400-154126400	Weak transcription	Primary B cells from cord blood	blood
28	chr1:154123400-154126600	Weak transcription	Fetal Thymus	thymus
29	chr1:154123400-154127000	Weak transcription	Lung	lung

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