Variant report

Variant	rs27389
Chromosome Location	chr5:50140456-50140457
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	chr5:50139685..50142220-chr5:50145007..50147004,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10035164	1.00[CHB][hapmap]
rs10036060	1.00[CHB][hapmap]
rs10044566	1.00[CHB][hapmap]
rs10053011	1.00[CHB][hapmap]
rs10054381	1.00[CHB][hapmap]
rs10056836	1.00[CHB][hapmap]
rs10059085	1.00[CHB][hapmap]
rs10075034	1.00[CHB][hapmap]
rs10085036	1.00[CHB][hapmap]
rs10755235	1.00[CHB][hapmap]
rs10940497	1.00[CHB][hapmap]
rs11750771	1.00[CHB][hapmap]
rs12188262	1.00[CHB][hapmap]
rs12188654	1.00[CHB][hapmap]
rs154137	1.00[CHB][hapmap]
rs154138	1.00[CHB][hapmap]
rs154140	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16884018	1.00[CHB][hapmap]
rs169497	0.82[CHB][hapmap]
rs182230	1.00[CHB][hapmap]
rs2548581	0.82[CHB][hapmap]
rs256340	1.00[CHB][hapmap]
rs256341	1.00[CHB][hapmap]
rs2594706	1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs26062	1.00[CHB][hapmap]
rs26065	1.00[CHB][hapmap]
rs26069	1.00[CHB][hapmap]
rs26071	1.00[CHB][hapmap]
rs27244	0.82[ASN][1000 genomes]
rs27466	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs27467	1.00[CHB][hapmap]
rs27468	1.00[CHB][hapmap]
rs27469	1.00[CHB][hapmap]
rs27606	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs27627	1.00[CHB][hapmap]
rs282545	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs282550	1.00[CHB][hapmap]
rs282553	1.00[CHB][hapmap]
rs282554	0.87[EUR][1000 genomes]
rs282561	1.00[CHB][hapmap]
rs32376	1.00[CHB][hapmap];0.84[AFR][1000 genomes]
rs32404	1.00[CHB][hapmap]
rs32425	1.00[CHB][hapmap]
rs39613	1.00[CHB][hapmap]
rs42284	1.00[CHB][hapmap]
rs4865628	1.00[CHB][hapmap]
rs6872496	1.00[CHB][hapmap]
rs6890519	1.00[CHB][hapmap]
rs6890869	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462159	chr5:49960673-50229851	Strong transcription Weak transcription Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv598108	chr5:49960673-50229851	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1034445	chr5:49986171-50492609	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv598116	chr5:50064292-50318550	Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs27389	LOC647121	Cis_1M	lymphoblastoid	RTeQTL
rs27389	PARP8	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:50091200-50140600	Weak transcription	Small Intestine	intestine
2	chr5:50108200-50142800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr5:50109400-50141800	Strong transcription	Monocytes-CD14+_RO01746	blood
4	chr5:50110000-50141800	Strong transcription	Primary T cells fromperipheralblood	blood
5	chr5:50110400-50143400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr5:50110400-50143600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:50111000-50140800	Strong transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:50111200-50141600	Strong transcription	Primary T helper cells fromperipheralblood	blood
9	chr5:50119200-50144200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:50124200-50145200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr5:50124400-50141400	Weak transcription	Fetal Intestine Large	intestine
12	chr5:50124400-50141600	Weak transcription	Colon Smooth Muscle	Colon
13	chr5:50125000-50140600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr5:50125200-50142800	Weak transcription	HMEC	breast
15	chr5:50125200-50143200	Weak transcription	Left Ventricle	heart
16	chr5:50125400-50149200	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:50125800-50143200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr5:50126400-50143200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:50129200-50148400	Weak transcription	GM12878-XiMat	blood
20	chr5:50130600-50141400	Strong transcription	Dnd41	blood
21	chr5:50130800-50141400	Weak transcription	Stomach Smooth Muscle	stomach
22	chr5:50132600-50141200	Weak transcription	Aorta	Aorta
23	chr5:50132600-50148400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:50132800-50142200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr5:50133200-50140800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr5:50133400-50150000	Weak transcription	Adipose Nuclei	Adipose
27	chr5:50137000-50141600	Strong transcription	Primary B cells from cord blood	blood
28	chr5:50137800-50140600	Strong transcription	Primary B cells from peripheral blood	blood
29	chr5:50137800-50140800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr5:50138600-50141400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr5:50138600-50144400	Weak transcription	Liver	Liver
32	chr5:50138800-50141400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:50139200-50143400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr5:50139600-50141000	Weak transcription	Ovary	ovary
35	chr5:50139800-50141400	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr5:50139800-50142600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:50140000-50141400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr5:50140000-50141600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr5:50140000-50141800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr5:50140000-50141800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
41	chr5:50140000-50142000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
42	chr5:50140000-50142800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr5:50140000-50142800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr5:50140000-50143400	Weak transcription	Primary T cells from cord blood	blood
45	chr5:50140000-50143400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr5:50140000-50144400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr5:50140200-50142000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr5:50140200-50148600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:50140400-50142600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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