Variant report

Variant	rs2609886
Chromosome Location	chr19:44803508-44803509
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:44803134..44806293-chr19:44806524..44808794,3	K562	blood:
2	chr19:44803407..44806293-chr19:44806642..44810099,5	K562	blood:
3	chr19:44802318..44803982-chr19:44806130..44808963,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159917	Chromatin interaction

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1233430	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233431	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233432	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233433	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233434	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233436	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233438	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233442	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233443	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233445	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233446	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233449	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233450	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233451	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233452	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233453	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233457	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1233458	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233460	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233461	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233462	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233469	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233471	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233472	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233473	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233474	0.87[TSI][hapmap];0.82[AMR][1000 genomes]
rs1234839	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1234840	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1235163	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1237178	0.93[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1237179	0.81[CEU][hapmap];1.00[GIH][hapmap];0.95[TSI][hapmap]
rs1238786	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1347349	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1369100	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16978991	0.80[CEU][hapmap]
rs17657025	0.85[CEU][hapmap]
rs2117385	0.81[CEU][hapmap]
rs2117387	0.81[CEU][hapmap]
rs2164112	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2164113	1.00[CEU][hapmap];0.91[YRI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2168990	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2196185	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249402	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2446491	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2571076	0.81[CEU][hapmap]
rs2571100	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2571105	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2571106	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609881	1.00[GIH][hapmap];0.86[MEX][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609883	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609887	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2609890	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2609892	1.00[GIH][hapmap];0.85[MKK][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609898	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2609905	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609906	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609907	1.00[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs2609909	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722707	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2722708	1.00[GIH][hapmap];0.80[MEX][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2722711	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2722715	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2722716	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2722717	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59555311	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6509153	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs874187	1.00[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs898175	1.00[GIH][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs898176	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs898177	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs898179	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs984116	0.91[AMR][1000 genomes];0.96[EUR][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	nsv961228	chr19:44803007-44803904	Genic enhancers Strong transcription Weak transcription ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2609886	SNORD33	cis	cerebellum	SCAN
rs2609886	SYT3	cis	cerebellum	SCAN
rs2609886	NKPD1	cis	cerebellum	SCAN
rs2609886	LIG1	cis	cerebellum	SCAN
rs2609886	PTGIR	cis	parietal	SCAN
rs2609886	ZNF473	cis	cerebellum	SCAN
rs2609886	FLT3LG	cis	cerebellum	SCAN
rs2609886	KLK7	cis	cerebellum	SCAN
rs2609886	FLT3LG	cis	parietal	SCAN
rs2609886	AKT1S1	cis	cerebellum	SCAN
rs2609886	ZFP112	trans	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44777000-44807000	ZNF genes & repeats	Liver	Liver
2	chr19:44783200-44804400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr19:44790400-44806800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr19:44790400-44808400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr19:44791200-44806800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:44791400-44804600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr19:44792400-44807600	Weak transcription	HUVEC	blood vessel
8	chr19:44792800-44807600	Weak transcription	NH-A	brain
9	chr19:44792800-44808400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:44794400-44806400	Strong transcription	Rectal Mucosa Donor 29	rectum
11	chr19:44794400-44806800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr19:44794600-44807600	Strong transcription	Primary B cells from cord blood	blood
13	chr19:44794800-44803600	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr19:44796800-44806800	Strong transcription	Brain Germinal Matrix	brain
15	chr19:44798400-44807000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr19:44798400-44807400	Strong transcription	Dnd41	blood
17	chr19:44798600-44806800	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr19:44798800-44804400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
19	chr19:44798800-44804400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr19:44799000-44804400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr19:44799000-44804600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr19:44799200-44805600	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr19:44799200-44806800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr19:44799400-44804600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr19:44799400-44806800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr19:44799400-44806800	Strong transcription	Fetal Kidney	kidney
27	chr19:44799600-44803800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr19:44799600-44804400	Strong transcription	Fetal Brain Male	brain
29	chr19:44799600-44804600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:44799600-44806800	Strong transcription	Placenta	Placenta
31	chr19:44799600-44806800	Strong transcription	Stomach Smooth Muscle	stomach
32	chr19:44799600-44807600	Strong transcription	Skeletal Muscle Female	skeletal muscle
33	chr19:44799800-44804400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
34	chr19:44799800-44804400	Strong transcription	HepG2	liver
35	chr19:44799800-44804600	Strong transcription	HUES64 Cell Line	embryonic stem cell
36	chr19:44799800-44807400	Weak transcription	K562	blood
37	chr19:44799800-44807600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr19:44800000-44803800	Strong transcription	Placenta Amnion	Placenta Amnion
39	chr19:44800000-44806800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr19:44800000-44806800	Strong transcription	Primary neutrophils fromperipheralblood	blood
41	chr19:44800000-44806800	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:44800200-44804400	Strong transcription	HUES6 Cell Line	embryonic stem cell
43	chr19:44800200-44806000	Strong transcription	A549	lung
44	chr19:44800200-44806200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr19:44800200-44806200	Strong transcription	Brain Hippocampus Middle	brain
46	chr19:44800200-44806200	Strong transcription	Rectal Smooth Muscle	rectum
47	chr19:44800200-44806400	Strong transcription	Brain Cingulate Gyrus	brain
48	chr19:44800200-44806800	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:44800200-44806800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr19:44800400-44806800	Strong transcription	iPS-20b Cell Line	embryonic stem cell

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