Variant report

Variant	rs1009381
Chromosome Location	chr19:36537959-36537960
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:36537347..36538989-chr19:36543422..36545265,2	K562	blood:
2	chr19:36537458..36539950-chr19:36540534..36542678,2	MCF-7	breast:
3	chr19:36498459..36500910-chr19:36535292..36537978,3	MCF-7	breast:
4	chr19:36537396..36539582-chr19:36543330..36546282,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075702	Chromatin interaction
ENSG00000181392	Chromatin interaction
ENSG00000161277	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10406862	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[ASN][1000 genomes]
rs10418079	0.90[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10420345	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10421377	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10422055	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10425700	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs11538454	0.85[ASN][1000 genomes]
rs11666192	0.81[ASN][1000 genomes]
rs11669890	0.92[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs12462159	1.00[CHB][hapmap];0.83[JPT][hapmap]
rs12608517	0.84[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.85[ASN][1000 genomes]
rs12981698	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.94[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];0.95[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1548506	0.80[CEU][hapmap]
rs2023866	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2051800	0.81[CEU][hapmap]
rs2074435	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2075472	0.93[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2227260	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2231568	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2301734	1.00[CHB][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2301737	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2871649	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[ASN][1000 genomes]
rs4555271	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs4806249	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[ASN][1000 genomes]
rs4806254	1.00[CHB][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap]
rs4806262	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4806273	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4806276	1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs55849299	0.87[ASN][1000 genomes]
rs7250364	0.81[ASN][1000 genomes]
rs7251912	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs7257026	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7258807	0.84[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.83[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs757223	0.81[CEU][hapmap]
rs8104047	0.81[EUR][1000 genomes]
rs8112640	0.81[ASN][1000 genomes]

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	nsv911638	chr19:36265508-36537959	Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs1009381	POLR2I	cis	multi-tissue	Pritchard
rs1009381	PHLDB3	cis	parietal	SCAN
rs1009381	CYP2A7	cis	cerebellum	SCAN
rs1009381	POLR2I///RPSA	Cis_1M	lymphoblastoid	RTeQTL
rs1009381	PSG9	cis	cerebellum	SCAN
rs1009381	CYP2A7	cis	parietal	SCAN
rs1009381	PHLDB3	cis	cerebellum	SCAN
rs1009381	LOC390940	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36506400-36544400	Weak transcription	GM12878-XiMat	blood
2	chr19:36515400-36544600	Weak transcription	Pancreas	Pancrea
3	chr19:36524200-36543800	Weak transcription	Left Ventricle	heart
4	chr19:36524200-36544000	Weak transcription	Primary B cells from cord blood	blood
5	chr19:36524200-36544400	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr19:36524200-36544400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr19:36524200-36544400	Weak transcription	Aorta	Aorta
8	chr19:36524400-36543800	Weak transcription	Primary B cells from peripheral blood	blood
9	chr19:36524400-36544000	Weak transcription	Fetal Lung	lung
10	chr19:36526400-36544200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr19:36526600-36540200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr19:36526600-36544400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr19:36526800-36544400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr19:36527000-36544600	Weak transcription	Gastric	stomach
15	chr19:36528400-36544000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:36528600-36543800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr19:36528600-36543800	Weak transcription	Fetal Thymus	thymus
18	chr19:36528600-36544000	Weak transcription	Primary hematopoietic stem cells	blood
19	chr19:36528600-36544000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:36528600-36544400	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr19:36528600-36544400	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr19:36530400-36544200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:36530400-36544400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr19:36530600-36543800	Weak transcription	Fetal Muscle Trunk	muscle
25	chr19:36530600-36544000	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr19:36530600-36544400	Weak transcription	Cortex derived primary cultured neurospheres	brain
27	chr19:36530800-36543800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr19:36530800-36543800	Weak transcription	Brain Germinal Matrix	brain
29	chr19:36530800-36543800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr19:36531000-36543800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr19:36531000-36543800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr19:36531000-36543800	Weak transcription	Fetal Muscle Leg	muscle
33	chr19:36531000-36544000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr19:36531000-36544000	Weak transcription	Esophagus	oesophagus
35	chr19:36531200-36543800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:36531200-36544000	Weak transcription	Duodenum Mucosa	Duodenum
37	chr19:36531400-36544000	Weak transcription	Spleen	Spleen
38	chr19:36531800-36541400	Weak transcription	Fetal Stomach	stomach
39	chr19:36531800-36543600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr19:36532600-36543800	Weak transcription	Fetal Intestine Large	intestine
41	chr19:36532800-36539800	Weak transcription	HMEC	breast
42	chr19:36532800-36539800	Weak transcription	NHEK	skin
43	chr19:36532800-36540000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr19:36532800-36543600	Weak transcription	Hela-S3	cervix
45	chr19:36533000-36544600	Weak transcription	Lung	lung
46	chr19:36533200-36544200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
47	chr19:36533200-36544400	Weak transcription	Fetal Heart	heart
48	chr19:36533200-36544400	Weak transcription	Placenta Amnion	Placenta Amnion
49	chr19:36533400-36542000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
50	chr19:36533400-36542000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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