Variant report

Variant	rs13187028
Chromosome Location	chr5:36886836-36886837
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	chr5:36876398..36879013-chr5:36886021..36888865,3	MCF-7	breast:
2	chr5:36728405..36730840-chr5:36886021..36888598,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164190	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs13156908	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13162626	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13163996	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13164726	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13165105	0.87[EUR][1000 genomes]
rs13176635	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13181330	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13181860	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13186745	0.89[EUR][1000 genomes]
rs1353256	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs165962	0.85[CEU][hapmap]
rs16903418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.96[LWK][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17312211	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs187391	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs188383	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs213513	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs245672	0.91[CEU][hapmap]
rs289216	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs293753	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293754	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs293775	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs298973	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34079524	0.89[EUR][1000 genomes]
rs34218486	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34272373	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34697946	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34807025	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34911537	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35127161	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35167018	0.95[EUR][1000 genomes]
rs35357341	0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35394109	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35809470	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36035695	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs36650	0.85[CEU][hapmap];0.87[TSI][hapmap]
rs36676	0.85[CEU][hapmap];0.84[TSI][hapmap]
rs3776594	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3899482	0.87[EUR][1000 genomes]
rs58123624	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62654860	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6868809	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6894622	0.89[EUR][1000 genomes]
rs71617772	0.93[EUR][1000 genomes]
rs71617774	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73093888	0.89[EUR][1000 genomes]
rs7700441	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7704442	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7716192	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs923957	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv492319	chr5:36570707-37061019	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv525478	chr5:36804225-37349895	Strong transcription Transcr. at gene 5' and 3' Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv532133	chr5:36834932-36906436	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	esv1793961	chr5:36866835-37361728	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
5	nsv964843	chr5:36885131-36887084	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
6	nsv530225	chr5:36886635-37331912	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13187028	C5orf42	cis	cerebellum	SCAN
rs13187028	TARS	cis	cerebellum	SCAN
rs13187028	IL7R	cis	cerebellum	SCAN

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:36879200-36889400	Enhancers	Primary T killer memory cells from peripheral blood	blood
2	chr5:36879400-36887400	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr5:36879600-36889400	Weak transcription	HSMMtube	muscle
4	chr5:36879800-36891400	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr5:36880000-36889000	Weak transcription	Brain Anterior Caudate	brain
6	chr5:36880000-36891200	Weak transcription	Fetal Brain Female	brain
7	chr5:36880000-36897400	Weak transcription	NHLF	lung
8	chr5:36880400-36897800	Weak transcription	HUVEC	blood vessel
9	chr5:36881000-36899800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:36881000-36900600	Weak transcription	Osteobl	bone
11	chr5:36881200-36887400	Weak transcription	HMEC	breast
12	chr5:36881200-36890600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:36881200-36892400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr5:36881200-36900400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr5:36881400-36897400	Weak transcription	NHDF-Ad	bronchial
16	chr5:36881600-36887200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr5:36881800-36895400	Weak transcription	Fetal Kidney	kidney
18	chr5:36882400-36899800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:36882600-36887600	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr5:36882800-36891400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:36883000-36887400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:36883200-36887400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr5:36883400-36887400	Weak transcription	Colon Smooth Muscle	Colon
24	chr5:36884000-36892000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr5:36884200-36889600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr5:36884600-36897200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr5:36884800-36887800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr5:36885000-36899200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr5:36885400-36888000	Enhancers	Liver	Liver
30	chr5:36885600-36888400	Enhancers	Fetal Heart	heart
31	chr5:36885800-36890800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr5:36885800-36890800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr5:36886000-36887400	Weak transcription	Stomach Mucosa	stomach
34	chr5:36886000-36887600	Weak transcription	H1 Cell Line	embryonic stem cell
35	chr5:36886000-36888400	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr5:36886000-36894800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr5:36886200-36887400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:36886200-36887400	Weak transcription	Brain Hippocampus Middle	brain
39	chr5:36886200-36887400	Weak transcription	K562	blood
40	chr5:36886200-36887800	Weak transcription	Brain Germinal Matrix	brain
41	chr5:36886200-36889600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr5:36886200-36889800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr5:36886200-36891400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr5:36886200-36891400	Weak transcription	Aorta	Aorta
45	chr5:36886200-36891400	Weak transcription	HSMM	muscle
46	chr5:36886200-36893200	Weak transcription	Placenta	Placenta
47	chr5:36886200-36893400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr5:36886200-36893400	Weak transcription	Fetal Muscle Trunk	muscle
49	chr5:36886200-36893600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr5:36886200-36894800	Weak transcription	Primary neutrophils fromperipheralblood	blood

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