Variant report

Variant	rs2609881
Chromosome Location	chr19:44831989-44831990
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44830119..44832268-chr19:44837781..44840582,2	K562	blood:
2	chr19:44807899..44809893-chr19:44829834..44832203,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159917	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:76)

rs_ID	r²[population]
rs1233430	1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233431	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1233432	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1233433	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233434	0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233436	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233438	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs1233442	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233443	0.91[EUR][1000 genomes]
rs1233445	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233446	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1233449	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233450	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1233451	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233452	1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap]
rs1233453	1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs1233457	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1233458	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233460	1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233461	1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233462	1.00[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233469	1.00[GIH][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes]
rs1233472	0.80[AMR][1000 genomes]
rs1233474	1.00[CEU][hapmap];0.95[TSI][hapmap];0.87[EUR][1000 genomes]
rs1234839	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1235163	1.00[GIH][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap]
rs1237178	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs1237179	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs1238786	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1347349	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1369100	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1836273	0.81[ASN][1000 genomes]
rs2164112	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2164113	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2168990	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2196185	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2249402	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2262860	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2446491	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2466421	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2571100	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2571104	0.86[YRI][hapmap]
rs2571105	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2571106	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609883	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609886	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]
rs2609887	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609889	0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2609890	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609892	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609898	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2609905	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2609906	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2609907	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap]
rs2609909	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2722707	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722708	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722711	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722715	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722716	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722717	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2722718	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2722719	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs2722721	1.00[CHD][hapmap];0.80[JPT][hapmap];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs2722735	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2722736	0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2722738	0.90[ASN][1000 genomes]
rs2722739	0.83[ASN][1000 genomes]
rs59555311	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6509153	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs874187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898175	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898176	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898177	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs898179	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs984116	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2609881	FLT3LG	cis	parietal	SCAN
rs2609881	GPR77	cis	cerebellum	SCAN
rs2609881	ZFP112	trans	cerebellum	SCAN
rs2609881	ZNF229	trans	cerebellum	SCAN
rs2609881	SYT3	cis	cerebellum	SCAN
rs2609881	SNORD33	cis	cerebellum	SCAN
rs2609881	ZNF473	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44823200-44856200	ZNF genes & repeats	Liver	Liver
2	chr19:44824800-44841000	ZNF genes & repeats	Adipose Nuclei	Adipose
3	chr19:44825000-44846600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
4	chr19:44827800-44832000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr19:44828000-44845000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
6	chr19:44828400-44846400	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
7	chr19:44828600-44832800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr19:44828600-44844200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr19:44828600-44845600	ZNF genes & repeats	Fetal Lung	lung
10	chr19:44828600-44848800	ZNF genes & repeats	Fetal Brain Female	brain
11	chr19:44828600-44851000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
12	chr19:44828800-44842600	ZNF genes & repeats	Duodenum Mucosa	Duodenum
13	chr19:44828800-44846200	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr19:44828800-44846400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:44829000-44832400	Weak transcription	Fetal Heart	heart
16	chr19:44829000-44844000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr19:44829200-44841200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr19:44830400-44845000	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr19:44830600-44841200	ZNF genes & repeats	Brain Germinal Matrix	brain
20	chr19:44830600-44845200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr19:44830800-44834000	ZNF genes & repeats	Brain Substantia Nigra	brain
22	chr19:44830800-44836000	ZNF genes & repeats	Fetal Brain Male	brain
23	chr19:44830800-44840800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
24	chr19:44830800-44845600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr19:44830800-44850400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr19:44831200-44832000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
27	chr19:44831200-44832200	Strong transcription	NHDF-Ad	bronchial
28	chr19:44831200-44832400	ZNF genes & repeats	Brain Angular Gyrus	brain
29	chr19:44831200-44834200	ZNF genes & repeats	Psoas Muscle	Psoas
30	chr19:44831200-44835000	Strong transcription	Cortex derived primary cultured neurospheres	brain
31	chr19:44831200-44836600	ZNF genes & repeats	Ovary	ovary
32	chr19:44831200-44838600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr19:44831400-44834200	ZNF genes & repeats	A549	lung
34	chr19:44831400-44834400	Strong transcription	Brain Hippocampus Middle	brain
35	chr19:44831400-44840000	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:44831600-44832200	ZNF genes & repeats	NH-A	brain
37	chr19:44831600-44832400	ZNF genes & repeats	Brain Cingulate Gyrus	brain
38	chr19:44831600-44832400	ZNF genes & repeats	Placenta	Placenta
39	chr19:44831600-44832600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
40	chr19:44831600-44832600	ZNF genes & repeats	Lung	lung
41	chr19:44831600-44832600	ZNF genes & repeats	Pancreas	Pancrea
42	chr19:44831600-44832600	ZNF genes & repeats	HSMM	muscle
43	chr19:44831600-44832800	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:44831600-44832800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:44831600-44832800	ZNF genes & repeats	Left Ventricle	heart
46	chr19:44831600-44832800	Strong transcription	Rectal Smooth Muscle	rectum
47	chr19:44831600-44833000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
48	chr19:44831600-44833200	ZNF genes & repeats	Spleen	Spleen
49	chr19:44831600-44833600	ZNF genes & repeats	Stomach Smooth Muscle	stomach
50	chr19:44831600-44833800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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