Variant report

Variant	rs9544006
Chromosome Location	chr13:76193470-76193471
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:76191703..76193489-chr13:76193582..76195230,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COMMD6-2	chr13:76193379-76193500	NONHSAT034366

Variant related genes	Relation type
ENSG00000136153	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10162224	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11617067	0.96[EUR][1000 genomes]
rs2274046	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4885329	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4885335	0.96[ASN][1000 genomes]
rs8001729	0.90[ASN][1000 genomes]
rs8192757	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8192761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9318359	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9318360	0.86[CEU][hapmap];1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9318362	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9530449	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530451	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9530452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9543963	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9543964	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9543967	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9543983	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs9543986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9543991	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9543995	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544000	0.91[AMR][1000 genomes]
rs9544001	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544003	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9544007	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9573582	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9573595	0.96[ASN][1000 genomes]
rs9593092	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9600487	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs9600494	0.95[EUR][1000 genomes]
rs9600498	1.00[ASN][1000 genomes]
rs9600504	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9600508	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9652173	0.85[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900571	chr13:76123678-76207565	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv900577	chr13:76132484-76207565	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	esv2751152	chr13:76144199-76288418	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9544006	UCHL3	cis	Artery Tibial	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76125000-76209600	Weak transcription	Right Ventricle	heart
2	chr13:76144200-76194400	Weak transcription	Stomach Smooth Muscle	stomach
3	chr13:76148200-76203000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:76148200-76209600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr13:76149800-76209600	Weak transcription	Lung	lung
6	chr13:76158600-76195200	Weak transcription	NHEK	skin
7	chr13:76159000-76194600	Weak transcription	HUVEC	blood vessel
8	chr13:76159000-76209600	Weak transcription	Brain Hippocampus Middle	brain
9	chr13:76159400-76201800	Weak transcription	Fetal Lung	lung
10	chr13:76164600-76194600	Weak transcription	Aorta	Aorta
11	chr13:76164600-76209400	Weak transcription	Esophagus	oesophagus
12	chr13:76165200-76209200	Weak transcription	Fetal Muscle Leg	muscle
13	chr13:76166800-76202000	Weak transcription	Fetal Brain Female	brain
14	chr13:76170800-76209600	Weak transcription	Primary B cells from peripheral blood	blood
15	chr13:76174600-76198200	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr13:76174600-76201400	Weak transcription	Psoas Muscle	Psoas
17	chr13:76176800-76199400	Weak transcription	Placenta	Placenta
18	chr13:76177600-76209400	Weak transcription	Left Ventricle	heart
19	chr13:76177600-76209600	Weak transcription	Fetal Stomach	stomach
20	chr13:76180000-76209600	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr13:76180600-76204000	Weak transcription	GM12878-XiMat	blood
22	chr13:76180800-76204600	Weak transcription	Dnd41	blood
23	chr13:76180800-76209200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:76180800-76209200	Weak transcription	Adipose Nuclei	Adipose
25	chr13:76180800-76209600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr13:76181000-76194600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:76181000-76209400	Weak transcription	Fetal Thymus	thymus
28	chr13:76181000-76209600	Weak transcription	Primary T helper cells fromperipheralblood	blood
29	chr13:76181000-76209600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:76181200-76194400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr13:76181200-76198200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr13:76181200-76209400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr13:76181200-76209600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
34	chr13:76181400-76199600	Weak transcription	Primary B cells from cord blood	blood
35	chr13:76181400-76199600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr13:76181600-76194600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr13:76181600-76207400	Weak transcription	HMEC	breast
38	chr13:76182200-76198200	Weak transcription	Primary hematopoietic stem cells	blood
39	chr13:76182800-76194200	Weak transcription	NH-A	brain
40	chr13:76182800-76209400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr13:76183000-76194400	Weak transcription	Fetal Heart	heart
42	chr13:76187400-76198000	Weak transcription	Primary T cells from cord blood	blood
43	chr13:76189600-76209400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr13:76190600-76209600	Weak transcription	Brain Angular Gyrus	brain
45	chr13:76191000-76201200	Weak transcription	Brain Anterior Caudate	brain
46	chr13:76191600-76201400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr13:76192000-76194200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr13:76192000-76194800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr13:76192000-76209600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr13:76192200-76209400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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