Variant report

Variant	rs11673222
Chromosome Location	chr19:38824344-38824345
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr19:38824203-38824713	HCT-116	colon:	n/a	n/a
2	POLR2A	chr19:38824020-38825234	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:38823410..38828693-chr19:38863569..38867873,9	K562	blood:
2	chr19:38824024..38830842-chr19:38863522..38868048,10	MCF-7	breast:
3	chr19:38819188..38821432-chr19:38824241..38826346,2	K562	blood:

Variant related genes	Relation type
CATSPERG	TF binding region
ENSG00000099341	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11668355	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11668651	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11669131	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11669230	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11671779	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11672219	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11672531	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[ASN][1000 genomes]
rs11672793	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11673012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11673203	0.88[ASN][1000 genomes]
rs12459746	0.89[CEU][hapmap];0.85[TSI][hapmap]
rs2270093	0.94[EUR][1000 genomes]
rs2270094	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs2270095	0.84[CEU][hapmap]
rs2286473	0.80[AMR][1000 genomes]
rs2286475	0.84[CEU][hapmap]
rs2286476	0.84[CEU][hapmap]
rs2286549	0.83[CHD][hapmap]
rs2302182	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2302183	0.97[ASN][1000 genomes]
rs2304176	0.84[CEU][hapmap]
rs2304177	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2368484	0.94[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2887262	0.94[AMR][1000 genomes]
rs34989303	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs35308902	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3745951	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3745952	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3816044	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs4386247	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs45437199	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4802326	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4802327	1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4802351	0.82[CEU][hapmap];0.82[GIH][hapmap]
rs4804016	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4804046	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs60082376	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7256575	0.80[AMR][1000 genomes]
rs73041302	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8101488	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8104823	0.88[MEX][hapmap]
rs8106900	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8112211	0.84[CEU][hapmap]
rs870218	0.88[MEX][hapmap]
rs931749	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs931750	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11673222	CYP2S1	cis	cerebellum	SCAN
rs11673222	SELV	cis	parietal	SCAN
rs11673222	APOC4	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38811200-38826200	Weak transcription	Brain Anterior Caudate	brain
2	chr19:38811200-38826600	Weak transcription	Brain Substantia Nigra	brain
3	chr19:38811400-38825600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr19:38812000-38826000	Weak transcription	Fetal Thymus	thymus
5	chr19:38812000-38826600	Weak transcription	HUVEC	blood vessel
6	chr19:38812200-38826400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
7	chr19:38812200-38826600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr19:38812400-38826400	Weak transcription	Primary hematopoietic stem cells	blood
9	chr19:38812400-38826400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr19:38812400-38826400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr19:38812600-38826200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr19:38813000-38826000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr19:38813000-38826400	Weak transcription	Stomach Mucosa	stomach
14	chr19:38813200-38826800	Weak transcription	Fetal Heart	heart
15	chr19:38813400-38826000	Weak transcription	Fetal Intestine Large	intestine
16	chr19:38814000-38826400	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr19:38814200-38826400	Weak transcription	Right Atrium	heart
18	chr19:38814600-38826400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr19:38815000-38826400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr19:38818000-38826600	Weak transcription	Small Intestine	intestine
21	chr19:38818200-38826600	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr19:38818400-38826000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr19:38818400-38826200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:38818400-38826600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr19:38818600-38826200	Weak transcription	Thymus	Thymus
26	chr19:38818600-38826400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr19:38818600-38826600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr19:38818800-38825800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr19:38818800-38826000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr19:38818800-38826000	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr19:38818800-38826400	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr19:38818800-38826400	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr19:38818800-38826400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr19:38818800-38826400	Weak transcription	Brain Hippocampus Middle	brain
35	chr19:38818800-38826600	Weak transcription	Fetal Lung	lung
36	chr19:38819000-38825800	Weak transcription	Fetal Muscle Trunk	muscle
37	chr19:38819000-38826000	Weak transcription	Fetal Muscle Leg	muscle
38	chr19:38819000-38826400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr19:38819000-38826400	Weak transcription	Colon Smooth Muscle	Colon
40	chr19:38819000-38826600	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr19:38819000-38826600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr19:38819000-38826600	Weak transcription	Rectal Smooth Muscle	rectum
43	chr19:38819200-38826000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:38819200-38826000	Weak transcription	HUES48 Cell Line	embryonic stem cell
45	chr19:38819200-38826000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr19:38819200-38826000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr19:38819200-38826000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr19:38819200-38826000	Weak transcription	HSMM	muscle
49	chr19:38819200-38826200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr19:38819200-38826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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