Variant report

Variant	rs6731562
Chromosome Location	chr2:172798262-172798263
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172798108..172800053-chr2:172949225..172950788,2	MCF-7	breast:
2	chr2:172777969..172779784-chr2:172796609..172799123,2	K562	blood:
3	chr2:172796815..172799164-chr2:172958912..172961164,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000128708	Chromatin interaction
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10165126	1.00[ASW][hapmap];0.87[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10167419	0.87[CEU][hapmap]
rs10174055	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs10194102	0.87[CEU][hapmap]
rs10201430	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10202823	1.00[CEU][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10930502	0.86[CEU][hapmap]
rs11757	0.87[CEU][hapmap]
rs11904009	0.87[CEU][hapmap]
rs12692973	0.87[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs12692974	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs12692978	0.93[ASW][hapmap];0.83[CEU][hapmap]
rs13004237	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs13030911	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2165934	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3770445	0.93[ASW][hapmap];0.83[CEU][hapmap];0.85[MEX][hapmap]
rs3770451	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs3770452	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs4667694	0.87[CEU][hapmap]
rs4668414	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs62182433	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6715929	0.87[ASW][hapmap];0.96[CEU][hapmap];0.83[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.90[TSI][hapmap];0.89[YRI][hapmap]
rs6724337	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs6725388	0.92[CEU][hapmap]
rs6727017	0.95[CEU][hapmap];0.88[EUR][1000 genomes]
rs6738445	0.83[CEU][hapmap]
rs6745143	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs6750058	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6752812	0.91[CEU][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs6754817	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs6758704	0.93[ASW][hapmap];0.86[CEU][hapmap];0.85[MEX][hapmap]
rs6759575	0.93[ASW][hapmap];0.87[CEU][hapmap];0.85[MEX][hapmap]
rs7563971	0.90[EUR][1000 genomes]
rs7564089	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7573003	0.87[CEU][hapmap]
rs7581072	0.83[AMR][1000 genomes]
rs7586207	0.93[ASW][hapmap];0.86[CEU][hapmap];0.85[MEX][hapmap]
rs7602037	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7608403	0.87[CEU][hapmap];0.86[MEX][hapmap]
rs908670	0.93[ASW][hapmap];0.83[CEU][hapmap];0.85[MEX][hapmap]
rs908671	0.83[CEU][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	nsv875410	chr2:172693780-172896587	Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
3	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs6731562	AC068039.4	cis	Esophagus Muscularis	GTEx
rs6731562	AC068039.4	cis	Skin Sun Exposed Lower leg	GTEx
rs6731562	AC068039.4	cis	Thyroid	GTEx
rs6731562	AC068039.4	cis	Nerve Tibial	GTEx
rs6731562	AC068039.4	cis	Muscle Skeletal	GTEx
rs6731562	AC068039.4	cis	lung	GTEx
rs6731562	SLC25A12	cis	Whole Blood	GTEx
rs6731562	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs6731562	SLC25A12	Cis_1M	lymphoblastoid	RTeQTL
rs6731562	AC068039.4	cis	Heart Left Ventricle	GTEx
rs6731562	AC068039.4	cis	Whole Blood	GTEx
rs6731562	AC068039.4	cis	Stomach	GTEx
rs6731562	AC068039.4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172779800-172828400	Weak transcription	Aorta	Aorta
2	chr2:172780000-172812800	Weak transcription	Lung	lung
3	chr2:172780000-172829000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:172780200-172822200	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:172780200-172840400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr2:172780400-172820600	Weak transcription	Brain Angular Gyrus	brain
7	chr2:172780400-172848800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr2:172780600-172811200	Weak transcription	HSMMtube	muscle
9	chr2:172780600-172811200	Weak transcription	NHEK	skin
10	chr2:172780600-172820600	Weak transcription	Brain Anterior Caudate	brain
11	chr2:172780600-172822200	Weak transcription	Liver	Liver
12	chr2:172780600-172822200	Weak transcription	Fetal Kidney	kidney
13	chr2:172780600-172847400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr2:172780600-172854200	Weak transcription	Small Intestine	intestine
15	chr2:172781000-172811000	Weak transcription	Right Ventricle	heart
16	chr2:172781000-172811200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr2:172781200-172801400	Weak transcription	NHDF-Ad	bronchial
18	chr2:172781200-172808800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr2:172781200-172811200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr2:172781400-172822000	Weak transcription	HUVEC	blood vessel
21	chr2:172783600-172851000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr2:172783800-172811200	Weak transcription	HMEC	breast
23	chr2:172784000-172804200	Weak transcription	Duodenum Mucosa	Duodenum
24	chr2:172784000-172811400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr2:172784200-172811200	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr2:172784600-172815000	Weak transcription	Left Ventricle	heart
27	chr2:172785000-172811200	Weak transcription	Adipose Nuclei	Adipose
28	chr2:172785400-172822200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr2:172785400-172822400	Weak transcription	Placenta	Placenta
30	chr2:172785800-172806400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
31	chr2:172785800-172822200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
32	chr2:172786200-172800600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr2:172787000-172804400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr2:172787000-172811400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr2:172787200-172812800	Weak transcription	Fetal Brain Male	brain
36	chr2:172787400-172810600	Weak transcription	Hela-S3	cervix
37	chr2:172787600-172809600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr2:172787800-172800400	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr2:172787800-172822200	Weak transcription	Brain Hippocampus Middle	brain
40	chr2:172788000-172804400	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr2:172788000-172806200	Weak transcription	Fetal Muscle Trunk	muscle
42	chr2:172788000-172809600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr2:172788000-172811400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:172788000-172811400	Weak transcription	Fetal Intestine Large	intestine
45	chr2:172788000-172811800	Weak transcription	Ovary	ovary
46	chr2:172788000-172812600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:172788200-172809600	Weak transcription	Thymus	Thymus
48	chr2:172788400-172803800	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:172788400-172810600	Weak transcription	GM12878-XiMat	blood
50	chr2:172788400-172811200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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