Variant report

Variant	rs4806280
Chromosome Location	chr19:36618526-36618527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:36617835..36619366-chr19:36705301..36707421,2	MCF-7	breast:
2	chr19:36583233..36586201-chr19:36617082..36618818,2	K562	blood:
3	chr19:36618311..36619273-chr19:36661263..36662378,12	K562	blood:
4	chr19:36618000..36620412-chr19:36704144..36708307,3	K562	blood:
5	chr19:36615077..36620423-chr19:36622100..36624907,6	K562	blood:
6	chr19:36617317..36620455-chr19:36659858..36661867,3	MCF-7	breast:
7	chr19:36618283..36619274-chr19:36661381..36662319,5	MCF-7	breast:
8	chr19:36610352..36613134-chr19:36616460..36619107,3	K562	blood:
9	chr19:36617223..36621168-chr19:36621174..36623571,4	MCF-7	breast:
10	chr19:36616979..36620071-chr19:36629993..36632800,4	K562	blood:
11	chr19:36617250..36625256-chr19:36625801..36633837,31	MCF-7	breast:
12	chr19:36612874..36616073-chr19:36617819..36620812,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105254	Chromatin interaction
ENSG00000167635	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000196357	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10407011	0.88[ASN][1000 genomes]
rs10426582	0.85[AMR][1000 genomes]
rs12462674	0.84[JPT][hapmap]
rs12972660	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12977802	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12979093	0.85[AMR][1000 genomes]
rs2023865	0.89[JPT][hapmap]
rs2072606	0.88[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.82[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2075474	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239510	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs34906485	0.80[AMR][1000 genomes]
rs3810445	0.90[JPT][hapmap];0.82[EUR][1000 genomes]
rs3826995	0.84[JPT][hapmap]
rs4805154	0.81[AMR][1000 genomes]
rs4805155	0.84[AMR][1000 genomes]
rs4806252	0.84[AMR][1000 genomes]
rs4806253	0.85[AMR][1000 genomes]
rs4806279	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56034793	0.85[AMR][1000 genomes]
rs62109743	0.85[AMR][1000 genomes]
rs7245762	0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7250448	0.82[MEX][hapmap];0.87[TSI][hapmap];0.85[AMR][1000 genomes]
rs7257383	0.89[JPT][hapmap];0.82[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8100250	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8103569	0.84[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	esv1831737	chr19:36324324-36690874	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv833815	chr19:36519803-36624936	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2752541	chr19:36563057-36690874	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4806280	PHLDB3	cis	parietal	SCAN
rs4806280	TEX101	cis	parietal	SCAN
rs4806280	PSG9	cis	cerebellum	SCAN
rs4806280	ZNF229	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36607200-36618600	Weak transcription	Psoas Muscle	Psoas
2	chr19:36607400-36618600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr19:36607400-36618800	Weak transcription	Small Intestine	intestine
4	chr19:36608200-36618600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:36614200-36618800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr19:36615200-36618600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr19:36615400-36618600	Weak transcription	Fetal Brain Male	brain
8	chr19:36616600-36618600	Weak transcription	HSMMtube	muscle
9	chr19:36616600-36619000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr19:36616800-36618600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr19:36616800-36618600	Weak transcription	NH-A	brain
12	chr19:36616800-36619000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr19:36617000-36618600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr19:36617000-36618600	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr19:36617000-36618600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr19:36617000-36618600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr19:36617000-36618600	Weak transcription	Primary T cells from cord blood	blood
18	chr19:36617000-36618600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr19:36617000-36618600	Weak transcription	Brain Germinal Matrix	brain
20	chr19:36617000-36618600	Weak transcription	Fetal Intestine Large	intestine
21	chr19:36617000-36618600	Weak transcription	Fetal Lung	lung
22	chr19:36617000-36618600	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr19:36617000-36618600	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr19:36617000-36618600	Weak transcription	Thymus	Thymus
25	chr19:36617000-36618800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr19:36617000-36618800	Weak transcription	Lung	lung
27	chr19:36617000-36618800	Weak transcription	Ovary	ovary
28	chr19:36617000-36619000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
29	chr19:36617000-36619000	Weak transcription	Aorta	Aorta
30	chr19:36617200-36618600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr19:36617200-36618600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr19:36617200-36618600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr19:36617200-36618600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
34	chr19:36617200-36618600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr19:36617200-36618600	Weak transcription	Spleen	Spleen
36	chr19:36617200-36618800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr19:36617200-36619000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr19:36617200-36619400	Weak transcription	Gastric	stomach
39	chr19:36618000-36618800	Flanking Active TSS	Dnd41	blood
40	chr19:36618200-36618600	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr19:36618200-36618600	Enhancers	Primary B cells from peripheral blood	blood
42	chr19:36618200-36618600	Enhancers	Primary T cells fromperipheralblood	blood
43	chr19:36618200-36618600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr19:36618200-36618600	Enhancers	Primary T helper cells PMA-I stimulated	--
45	chr19:36618200-36618600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
46	chr19:36618200-36618600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
47	chr19:36618200-36618600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr19:36618200-36618600	Enhancers	Fetal Muscle Trunk	muscle
49	chr19:36618200-36618600	Enhancers	Fetal Muscle Leg	muscle
50	chr19:36618200-36618600	Enhancers	Fetal Thymus	thymus

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