Variant report

Variant	rs2028270
Chromosome Location	chr5:79424938-79424939
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79423046..79425756-chr5:79550269..79553191,3	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-THBS4-3	chr5:79424746-79425020	ENSG00000251675.1

Variant related genes	Relation type
ENSG00000164300	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11950944	0.94[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12523350	0.90[ASN][1000 genomes]
rs13167875	0.83[ASN][1000 genomes]
rs1863959	0.90[ASN][1000 genomes]
rs4703798	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs4704611	0.90[ASN][1000 genomes]
rs4704613	0.81[ASN][1000 genomes]
rs4704614	0.83[ASN][1000 genomes]
rs6867810	0.81[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432748	chr5:79300434-79577760	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2028270	SERINC5	cis	multi-tissue	Pritchard

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79410000-79430800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr5:79417000-79437000	Weak transcription	Pancreas	Pancrea
3	chr5:79417400-79425400	Enhancers	Primary monocytes fromperipheralblood	blood
4	chr5:79417400-79430400	Weak transcription	Dnd41	blood
5	chr5:79419600-79435200	Weak transcription	Liver	Liver
6	chr5:79420800-79437000	Weak transcription	Lung	lung
7	chr5:79421000-79437000	Weak transcription	Fetal Brain Male	brain
8	chr5:79421200-79435400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:79421200-79436800	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr5:79421600-79428600	Weak transcription	Thymus	Thymus
11	chr5:79421600-79435800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:79421600-79438800	Weak transcription	Esophagus	oesophagus
13	chr5:79421800-79427000	Weak transcription	Primary T cells fromperipheralblood	blood
14	chr5:79421800-79430800	Weak transcription	Spleen	Spleen
15	chr5:79422200-79427400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr5:79422200-79429600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr5:79422400-79427600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:79423000-79427200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
19	chr5:79423200-79426400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr5:79423200-79427000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr5:79423200-79427400	Weak transcription	Primary T helper cells PMA-I stimulated	--
22	chr5:79423200-79427600	Weak transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:79423400-79427400	Weak transcription	Primary T cells from cord blood	blood
24	chr5:79423400-79430600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr5:79423400-79437000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:79423800-79425000	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr5:79423800-79425000	Enhancers	HSMMtube	muscle
28	chr5:79424000-79425000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:79424000-79425000	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr5:79424000-79425000	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr5:79424000-79425000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr5:79424000-79425200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr5:79424000-79425200	Enhancers	HUES6 Cell Line	embryonic stem cell
34	chr5:79424000-79425200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr5:79424000-79425200	Enhancers	Fetal Heart	heart
36	chr5:79424000-79425200	Enhancers	Placenta	Placenta
37	chr5:79424000-79425200	Enhancers	Fetal Stomach	stomach
38	chr5:79424000-79425400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
39	chr5:79424000-79425400	Enhancers	Fetal Kidney	kidney
40	chr5:79424000-79425400	Enhancers	Fetal Muscle Leg	muscle
41	chr5:79424000-79425400	Enhancers	HepG2	liver
42	chr5:79424200-79425000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr5:79424200-79425000	Enhancers	H9 Cell Line	embryonic stem cell
44	chr5:79424200-79425200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr5:79424200-79425200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
46	chr5:79424200-79425400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr5:79424200-79437000	Weak transcription	Fetal Muscle Trunk	muscle
48	chr5:79424200-79437200	Weak transcription	NHEK	skin
49	chr5:79424400-79425600	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr5:79424400-79436800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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