Variant report

Variant	rs1233434
Chromosome Location	chr19:44789124-44789125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:44788129..44789786-chr19:44790897..44793362,2	K562	blood:
2	chr19:44764025..44766893-chr19:44787287..44789375,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159915	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs1233430	0.92[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[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	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1233433	0.92[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];0.88[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	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1233446	0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233449	1.00[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233450	0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233451	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233452	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1233453	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][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	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233460	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233461	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[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];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233469	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233471	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1233472	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233473	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1233474	0.87[TSI][hapmap]
rs1234839	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1234840	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1235163	1.00[CEU][hapmap];0.93[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1237178	0.93[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1237179	0.81[CEU][hapmap];0.93[GIH][hapmap];0.95[TSI][hapmap]
rs1238786	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1347349	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1369100	0.82[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	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2164113	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2168990	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2196185	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2249402	0.88[EUR][1000 genomes]
rs2446491	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2571076	0.81[CEU][hapmap]
rs2571100	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2571105	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2571106	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2609881	0.93[GIH][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609883	0.88[EUR][1000 genomes]
rs2609886	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]
rs2609887	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2609890	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2609892	0.93[GIH][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2609898	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2609905	0.88[EUR][1000 genomes]
rs2609906	0.88[EUR][1000 genomes]
rs2609907	0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs2609909	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2722707	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2722708	0.93[GIH][hapmap];0.85[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs2722711	0.88[EUR][1000 genomes]
rs2722715	0.88[EUR][1000 genomes]
rs2722716	0.88[EUR][1000 genomes]
rs2722717	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs59555311	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6509153	0.88[EUR][1000 genomes]
rs874187	0.93[GIH][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs898175	0.93[GIH][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes]
rs898176	0.88[EUR][1000 genomes]
rs898177	0.88[EUR][1000 genomes]
rs898179	0.85[EUR][1000 genomes]
rs984116	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1233434	FLT3LG	cis	cerebellum	SCAN
rs1233434	NKPD1	cis	cerebellum	SCAN
rs1233434	ZNF473	cis	cerebellum	SCAN
rs1233434	ZFP112	trans	cerebellum	SCAN
rs1233434	SNORD33	cis	cerebellum	SCAN
rs1233434	AKT1S1	cis	cerebellum	SCAN
rs1233434	FLT3LG	cis	parietal	SCAN
rs1233434	KLK7	cis	cerebellum	SCAN
rs1233434	SYT3	cis	cerebellum	SCAN
rs1233434	RUVBL2	cis	parietal	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44775000-44791200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr19:44777000-44807000	ZNF genes & repeats	Liver	Liver
3	chr19:44778800-44791000	Weak transcription	Fetal Heart	heart
4	chr19:44778800-44791000	Weak transcription	HSMMtube	muscle
5	chr19:44778800-44791400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr19:44779200-44789200	Weak transcription	Brain Angular Gyrus	brain
7	chr19:44779400-44791000	Weak transcription	Dnd41	blood
8	chr19:44781800-44801400	ZNF genes & repeats	Adipose Nuclei	Adipose
9	chr19:44782800-44791400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr19:44782800-44792000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr19:44783200-44791400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr19:44783200-44804400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr19:44785200-44791400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr19:44785200-44801600	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
15	chr19:44785600-44791200	Weak transcription	Right Ventricle	heart
16	chr19:44786000-44791200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr19:44787000-44790600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr19:44787400-44790400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr19:44787400-44790800	Weak transcription	Fetal Brain Male	brain
20	chr19:44787400-44791000	Weak transcription	Primary B cells from cord blood	blood
21	chr19:44787400-44791200	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr19:44787400-44791400	Weak transcription	NHEK	skin
23	chr19:44787400-44791600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr19:44787600-44790800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr19:44787600-44791200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:44787600-44791200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr19:44787600-44791400	Weak transcription	Brain Hippocampus Middle	brain
28	chr19:44787600-44791400	Weak transcription	HMEC	breast
29	chr19:44787600-44792000	Weak transcription	NHDF-Ad	bronchial
30	chr19:44788000-44790400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr19:44788000-44799800	Weak transcription	HepG2	liver
32	chr19:44788200-44790800	Enhancers	Rectal Smooth Muscle	rectum
33	chr19:44788200-44791000	Weak transcription	Cortex derived primary cultured neurospheres	brain
34	chr19:44788200-44791000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr19:44788200-44801600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
36	chr19:44788400-44791000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr19:44788400-44791200	Weak transcription	Pancreas	Pancrea
38	chr19:44788600-44791200	Weak transcription	Placenta	Placenta
39	chr19:44788600-44791400	Weak transcription	Fetal Stomach	stomach
40	chr19:44788800-44790200	ZNF genes & repeats	Colon Smooth Muscle	Colon
41	chr19:44788800-44791200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr19:44788800-44795400	ZNF genes & repeats	Stomach Smooth Muscle	stomach
43	chr19:44789000-44789200	Strong transcription	Fetal Brain Female	brain
44	chr19:44789000-44791600	Weak transcription	Fetal Thymus	thymus

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