Variant report

Variant	rs2153536
Chromosome Location	chr6:54156080-54156081
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11751405	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1316575	0.96[CEU][hapmap];0.87[GIH][hapmap];0.82[MKK][hapmap];0.80[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs1340670	0.84[GIH][hapmap]
rs1396380	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1508633	0.89[EUR][1000 genomes]
rs1508642	0.83[GIH][hapmap]
rs1605674	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17574067	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2136135	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2136136	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2153537	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2185506	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297983	0.87[MEX][hapmap]
rs2397156	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2840308	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3756808	0.92[CEU][hapmap];0.82[GIH][hapmap];0.81[MKK][hapmap];0.81[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs3798276	0.87[MEX][hapmap]
rs4142450	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4415156	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4712061	0.96[CEU][hapmap];0.95[GIH][hapmap];0.83[TSI][hapmap];0.85[YRI][hapmap];0.89[EUR][1000 genomes]
rs4715450	0.89[CHB][hapmap];0.91[MEX][hapmap]
rs62396368	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6458990	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763301	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7763740	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7767969	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7769117	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7771868	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7775058	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9349702	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370282	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9370283	0.96[CEU][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes]
rs9370286	0.87[MEX][hapmap]
rs9370288	0.82[MEX][hapmap]
rs9395931	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs991287	0.88[EUR][1000 genomes]

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	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv885888	chr6:54132353-54266032	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2153536	TINAG	Cis_1M	lymphoblastoid	RTeQTL
rs2153536	HCRTR2	cis	parietal	SCAN
rs2153536	GSTA1	cis	parietal	SCAN
rs2153536	TINAG	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:54152600-54157400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr6:54153200-54157600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:54153800-54160000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:54154800-54157600	Enhancers	HUVEC	blood vessel
5	chr6:54154800-54157800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr6:54155400-54156200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr6:54155400-54156800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr6:54155400-54156800	Enhancers	HSMM	muscle
9	chr6:54155400-54156800	Enhancers	HSMMtube	muscle
10	chr6:54155400-54156800	Enhancers	NH-A	brain
11	chr6:54155400-54157000	Enhancers	NHLF	lung
12	chr6:54155400-54157200	Enhancers	NHDF-Ad	bronchial
13	chr6:54155400-54157400	Enhancers	Muscle Satellite Cultured Cells	--
14	chr6:54155600-54157000	Enhancers	Osteobl	bone
15	chr6:54155800-54156200	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr6:54155800-54156200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr6:54155800-54156400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr6:54155800-54156400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr6:54155800-54156600	Flanking Active TSS	NHEK	skin
20	chr6:54156000-54156200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
21	chr6:54156000-54156200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr6:54156000-54156200	Flanking Active TSS	HMEC	breast
23	chr6:54156000-54156400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:54156000-54156400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
25	chr6:54156000-54156600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr6:54156000-54157000	Enhancers	HUES6 Cell Line	embryonic stem cell
27	chr6:54156000-54157000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr6:54156000-54157600	Enhancers	ES-I3 Cell Line	embryonic stem cell
29	chr6:54156000-54158400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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