Variant report

Variant	rs2897390
Chromosome Location	chr5:80530817-80530818
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:80530046..80533018-chr5:80537820..80540645,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000248794	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs10036376	0.85[CEU][hapmap]
rs10038684	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10041063	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[LWK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10053706	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10066296	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10073527	0.81[CEU][hapmap]
rs10078279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10474656	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10514213	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514215	0.85[CEU][hapmap]
rs1055383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[YRI][hapmap];0.83[AMR][1000 genomes]
rs10942945	0.93[CEU][hapmap];1.00[CHB][hapmap];0.80[YRI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950033	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12516414	0.81[CEU][hapmap]
rs13362314	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1566432	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16876403	0.81[CEU][hapmap]
rs17294418	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17294956	0.85[CEU][hapmap]
rs2270823	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.92[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2270824	0.81[CEU][hapmap]
rs28464111	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28650401	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2897389	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4703827	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704707	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704708	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4704710	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704712	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704715	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4704717	0.81[CEU][hapmap]
rs4704720	0.84[AMR][1000 genomes]
rs545	0.81[CEU][hapmap]
rs59132806	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60488995	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60904680	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs61244991	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6866499	0.95[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6885028	1.00[CHB][hapmap]
rs6893467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73130869	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7448717	0.94[CEU][hapmap]
rs750728	0.85[CEU][hapmap]
rs7709071	1.00[CHB][hapmap]
rs7709149	1.00[CHB][hapmap]
rs7720009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7728465	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734902	1.00[CHB][hapmap]
rs921928	1.00[CHB][hapmap]
rs9293841	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
2	nsv598750	chr5:80503528-80599578	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs2897390	CKMT2	cis	normal skin	skin_eQTL
rs2897390	CTC-281B15.1	cis	Adipose Subcutaneous	GTEx
rs2897390	CTD-2248H3.1	cis	Thyroid	GTEx
rs2897390	CTC-281B15.1	cis	Artery Aorta	GTEx
rs2897390	BHMT2	cis	cerebellum	SCAN
rs2897390	CTD-2248H3.1	cis	Artery Aorta	GTEx
rs2897390	CTC-281B15.1	cis	Thyroid	GTEx
rs2897390	CTC-281B15.1	cis	Esophagus Muscularis	GTEx
rs2897390	CTC-281B15.1	cis	Esophagus Mucosa	GTEx
rs2897390	CTC-281B15.1	cis	Nerve Tibial	GTEx
rs2897390	CTC-281B15.1	cis	lung	GTEx
rs2897390	CTD-2248H3.1	cis	Esophagus Mucosa	GTEx
rs2897390	CTD-2248H3.1	cis	lung	GTEx
rs2897390	CTD-2248H3.1	cis	Adipose Subcutaneous	GTEx
rs2897390	CTC-281B15.1	cis	Stomach	GTEx

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:80525800-80531000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr5:80526600-80531200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr5:80527000-80546200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr5:80528000-80564400	Weak transcription	Hela-S3	cervix
5	chr5:80528200-80531000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:80528200-80531800	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr5:80528400-80531600	Enhancers	Spleen	Spleen
8	chr5:80528600-80531400	Enhancers	Primary T cells fromperipheralblood	blood
9	chr5:80528600-80531600	Enhancers	Fetal Thymus	thymus
10	chr5:80528600-80532000	Enhancers	Lung	lung
11	chr5:80528800-80531000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr5:80528800-80531400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr5:80528800-80531400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr5:80529400-80531400	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr5:80529400-80531600	Weak transcription	Gastric	stomach
16	chr5:80529400-80531800	Weak transcription	Fetal Brain Female	brain
17	chr5:80529400-80532400	Weak transcription	Placenta	Placenta
18	chr5:80529400-80532400	Active TSS	Right Ventricle	heart
19	chr5:80529400-80535200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr5:80529400-80540800	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr5:80529400-80541000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr5:80529400-80543400	Weak transcription	NHLF	lung
23	chr5:80529400-80544200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr5:80529400-80549400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr5:80529600-80531000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr5:80529600-80531000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:80529600-80531000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:80529600-80531200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
29	chr5:80529600-80531200	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr5:80529600-80531200	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr5:80529600-80531200	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr5:80529600-80531200	Weak transcription	Fetal Lung	lung
33	chr5:80529600-80531200	Enhancers	HepG2	liver
34	chr5:80529600-80531200	Weak transcription	K562	blood
35	chr5:80529600-80531400	Weak transcription	Stomach Mucosa	stomach
36	chr5:80529600-80532000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr5:80529600-80532200	Enhancers	Adipose Nuclei	Adipose
38	chr5:80529600-80532400	Enhancers	Brain Anterior Caudate	brain
39	chr5:80529600-80535000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr5:80529600-80541000	Weak transcription	Fetal Intestine Large	intestine
41	chr5:80529600-80542800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr5:80529600-80545800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr5:80529800-80531000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr5:80529800-80531200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr5:80529800-80531200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr5:80529800-80531200	Enhancers	Aorta	Aorta
47	chr5:80529800-80531800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr5:80529800-80531800	Enhancers	HSMMtube	muscle
49	chr5:80529800-80532200	Enhancers	Ovary	ovary
50	chr5:80529800-80532400	Enhancers	Brain Angular Gyrus	brain

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