Variant report

Variant	rs698752
Chromosome Location	chr2:54453810-54453811
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:54448522..54450800-chr2:54452364..54454802,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1099252	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1099254	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11895807	0.87[ASN][1000 genomes]
rs1215143	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1358367	0.81[EUR][1000 genomes]
rs1682102	0.83[CHB][hapmap]
rs1682108	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1682111	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17045690	0.88[ASN][1000 genomes]
rs1727504	0.87[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1727527	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2695649	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs698751	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs843646	0.83[YRI][hapmap]
rs843648	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs843653	0.87[ASW][hapmap];0.90[LWK][hapmap];0.81[YRI][hapmap];0.86[AFR][1000 genomes]
rs843654	0.84[AFR][1000 genomes]
rs843656	0.83[AFR][1000 genomes]
rs843662	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs843663	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs843666	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs843671	0.89[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs843672	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[JPT][hapmap]
rs843689	0.81[AFR][1000 genomes]
rs843703	0.83[AFR][1000 genomes]
rs843705	0.87[ASW][hapmap];0.90[LWK][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes]
rs843720	0.83[CHB][hapmap]
rs843721	0.83[CHB][hapmap]
rs843722	0.83[CHB][hapmap]
rs843730	0.83[CHB][hapmap]
rs843731	0.83[CHB][hapmap]
rs843740	0.94[CHB][hapmap];0.81[JPT][hapmap]
rs843754	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs843756	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs843760	0.87[EUR][1000 genomes]
rs843762	0.83[YRI][hapmap];0.88[AFR][1000 genomes]
rs843763	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs843764	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs843765	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs843767	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs860057	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863622	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.88[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003205	chr2:54220049-54700843	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	esv2762639	chr2:54220049-54700855	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1011790	chr2:54220049-54714553	Flanking Active TSS ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv1002891	chr2:54227005-54682169	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	nsv535722	chr2:54227005-54682169	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
6	nsv1011690	chr2:54255361-54700843	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
7	nsv1000652	chr2:54345892-54469703	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv1009828	chr2:54393122-54488721	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
9	nsv525086	chr2:54432222-54459211	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv532512	chr2:54453210-54630755	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs698752	EPS8	trans	lymphoblastoid	seeQTL
rs698752	EFEMP1	cis	cerebellum	SCAN
rs698752	RPL23AP32	cis	cerebellum	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:54387800-54457400	Weak transcription	Aorta	Aorta
2	chr2:54442200-54456400	Weak transcription	Liver	Liver
3	chr2:54448600-54459400	Weak transcription	Esophagus	oesophagus
4	chr2:54448800-54459400	Weak transcription	HSMM	muscle
5	chr2:54449800-54535200	Weak transcription	Primary T cells from cord blood	blood
6	chr2:54450200-54454600	Weak transcription	Gastric	stomach
7	chr2:54450200-54455800	Weak transcription	Psoas Muscle	Psoas
8	chr2:54451600-54459400	Weak transcription	Left Ventricle	heart
9	chr2:54452400-54468000	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr2:54452600-54454000	Enhancers	Brain Anterior Caudate	brain
11	chr2:54452800-54490200	Weak transcription	Primary B cells from cord blood	blood
12	chr2:54453000-54454000	Enhancers	Adipose Nuclei	Adipose
13	chr2:54453000-54454000	Enhancers	HepG2	liver
14	chr2:54453000-54454200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr2:54453000-54456800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:54453200-54454000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:54453200-54454000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:54453200-54454000	Enhancers	Fetal Lung	lung
19	chr2:54453200-54454000	Enhancers	HUVEC	blood vessel
20	chr2:54453200-54454400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:54453400-54454000	Enhancers	HUES6 Cell Line	embryonic stem cell
22	chr2:54453400-54454000	Enhancers	Ovary	ovary
23	chr2:54453600-54454000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:54453600-54454000	Active TSS	Brain Angular Gyrus	brain
25	chr2:54453600-54454600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr2:54453600-54455000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:54453600-54455000	Weak transcription	Fetal Heart	heart
28	chr2:54453600-54455800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr2:54453600-54459000	Weak transcription	HMEC	breast
30	chr2:54453800-54454000	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr2:54453800-54454200	Enhancers	Brain Hippocampus Middle	brain
32	chr2:54453800-54454200	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr2:54453800-54454200	Enhancers	Brain Substantia Nigra	brain
34	chr2:54453800-54456000	Weak transcription	Fetal Kidney	kidney
35	chr2:54453800-54456200	Weak transcription	Osteobl	bone
36	chr2:54453800-54460400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr2:54453800-54466200	Weak transcription	Skeletal Muscle Female	skeletal muscle

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