Variant report

Variant	rs10752613
Chromosome Location	chr1:153760104-153760105
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153759800..153761704-chr1:153893842..153895431,2	K562	blood:
2	chr1:153754517..153758077-chr1:153759140..153763614,7	K562	blood:
3	chr1:153753211..153758068-chr1:153759455..153763614,7	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10127983	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.81[TSI][hapmap]
rs10559	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs10796956	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10908557	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs10908558	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs1110165	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs11264532	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11264680	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs11264743	0.89[CHD][hapmap];0.82[GIH][hapmap]
rs11581644	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs11583896	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11589857	0.80[CEU][hapmap];0.82[CHB][hapmap]
rs11590099	0.83[CEU][hapmap];0.82[CHB][hapmap]
rs12022158	0.82[CEU][hapmap];0.82[CHB][hapmap]
rs12022730	0.81[CHB][hapmap]
rs12028398	0.84[CEU][hapmap];0.81[CHB][hapmap]
rs12032914	0.84[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs12033835	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs12041920	0.89[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12042562	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs12042989	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs12043350	0.84[CEU][hapmap];0.82[CHB][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs12401565	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs12403956	0.89[CHD][hapmap];0.82[GIH][hapmap]
rs1572788	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs3748848	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs3791187	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap]
rs4077168	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4363451	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4391701	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4845357	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs4845583	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs6680140	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs72694220	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7512766	0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7537691	0.84[CEU][hapmap];0.82[CHB][hapmap]
rs8450	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap]
rs946682	0.84[CEU][hapmap];0.82[CHB][hapmap];0.89[CHD][hapmap];0.82[GIH][hapmap];0.91[MEX][hapmap];0.86[TSI][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	nsv1011897	chr1:153613597-153836703	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS 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 miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	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
3	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
4	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
5	nsv464039	chr1:153708906-153801098	Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv547941	chr1:153708906-153801098	Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
7	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	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
9	nsv515962	chr1:153752139-153773429	Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs10752613	HAX1	cis	parietal	SCAN
rs10752613	SMCP	cis	parietal	SCAN
rs10752613	GATAD2B	cis	cerebellum	SCAN
rs10752613	CRTC2	cis	multi-tissue	Pritchard
rs10752613	FLG	cis	parietal	SCAN
rs10752613	LASS2	cis	parietal	SCAN
rs10752613	SPRR2D	cis	parietal	SCAN
rs10752613	SLC27A3	cis	cerebellum	SCAN
rs10752613	SCNM1	cis	cerebellum	SCAN
rs10752613	ZNF606	trans	cerebellum	SCAN

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153756600-153761400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:153756600-153761800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr1:153756600-153761800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:153756600-153762000	Weak transcription	Brain Angular Gyrus	brain
5	chr1:153756600-153762200	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr1:153756600-153764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr1:153756600-153767000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr1:153756800-153760400	Weak transcription	Fetal Lung	lung
9	chr1:153756800-153760800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr1:153756800-153760800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr1:153756800-153761200	Weak transcription	Fetal Stomach	stomach
12	chr1:153756800-153761400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:153756800-153761400	Weak transcription	Liver	Liver
14	chr1:153756800-153761400	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr1:153756800-153761400	Weak transcription	Thymus	Thymus
16	chr1:153756800-153761600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr1:153756800-153761600	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:153756800-153761800	Weak transcription	Primary T cells from cord blood	blood
19	chr1:153756800-153761800	Weak transcription	Primary hematopoietic stem cells	blood
20	chr1:153756800-153761800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
21	chr1:153756800-153761800	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr1:153756800-153761800	Weak transcription	Adipose Nuclei	Adipose
23	chr1:153756800-153761800	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr1:153756800-153761800	Weak transcription	Duodenum Mucosa	Duodenum
25	chr1:153756800-153761800	Weak transcription	Fetal Thymus	thymus
26	chr1:153756800-153761800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr1:153756800-153761800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr1:153756800-153762000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:153756800-153762000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr1:153756800-153762000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr1:153756800-153762000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr1:153756800-153762000	Weak transcription	Brain Anterior Caudate	brain
33	chr1:153756800-153762000	Weak transcription	Brain Hippocampus Middle	brain
34	chr1:153756800-153762000	Weak transcription	Stomach Mucosa	stomach
35	chr1:153756800-153762000	Weak transcription	Osteobl	bone
36	chr1:153756800-153762200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr1:153756800-153763200	Weak transcription	K562	blood
38	chr1:153756800-153764200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:153757000-153761200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr1:153757000-153761400	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr1:153757000-153761400	Weak transcription	Monocytes-CD14+_RO01746	blood
42	chr1:153757000-153761800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr1:153757000-153761800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr1:153757000-153779200	Weak transcription	Dnd41	blood
45	chr1:153758400-153760400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr1:153758400-153762600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr1:153758600-153761400	Weak transcription	Primary B cells from cord blood	blood
48	chr1:153758800-153761800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr1:153759200-153761400	Weak transcription	GM12878-XiMat	blood

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