Variant report

Variant	rs1233446
Chromosome Location	chr19:44763634-44763635
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	SIX5	chr19:44763614-44764440	A549	lung:	n/a	n/a
2	GABPA	chr19:44763550-44764666	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:44763153..44765827-chr19:44767005..44769957,2	MCF-7	breast:
2	chr19:44762662..44765169-chr19:44806024..44808707,2	K562	blood:
3	chr19:44763163..44765702-chr19:44978103..44979674,2	MCF-7	breast:

Variant related genes	Relation type
ZNF233	TF binding region
ENSG00000159915	Chromatin interaction
ENSG00000159917	Chromatin interaction
ENSG00000267242	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	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1233431	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233432	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233433	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1233434	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]
rs1233435	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1233436	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233442	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1233443	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1233445	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233449	1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233451	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233452	1.00[GIH][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes]
rs1233453	1.00[GIH][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes]
rs1233457	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233458	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233460	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233461	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233462	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1233469	1.00[GIH][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1233471	0.88[AMR][1000 genomes]
rs1233472	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1233473	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1233474	1.00[CEU][hapmap];0.86[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1234839	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1234840	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1235163	1.00[GIH][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1237178	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1237179	1.00[GIH][hapmap];0.86[TSI][hapmap]
rs1238786	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1347349	0.85[EUR][1000 genomes]
rs1369100	0.86[EUR][1000 genomes]
rs2164112	0.85[EUR][1000 genomes]
rs2164113	0.86[EUR][1000 genomes]
rs2168990	0.86[EUR][1000 genomes]
rs2196185	0.85[EUR][1000 genomes]
rs2249402	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2446491	0.86[EUR][1000 genomes]
rs2466421	0.83[AMR][1000 genomes]
rs2571100	0.86[EUR][1000 genomes]
rs2571105	0.85[EUR][1000 genomes]
rs2571106	0.94[EUR][1000 genomes]
rs2609881	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2609883	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2609886	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]
rs2609887	0.86[EUR][1000 genomes]
rs2609890	0.85[EUR][1000 genomes]
rs2609892	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs2609898	0.86[EUR][1000 genomes]
rs2609905	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2609906	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2609907	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap]
rs2609909	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2722707	0.86[EUR][1000 genomes]
rs2722708	1.00[CEU][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2722711	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2722715	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2722716	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2722717	0.86[EUR][1000 genomes]
rs2722718	0.83[AMR][1000 genomes]
rs2722719	0.83[AMR][1000 genomes]
rs2722721	0.87[MEX][hapmap]
rs59555311	0.86[EUR][1000 genomes]
rs6509153	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs874187	1.00[CEU][hapmap];1.00[GIH][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898175	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898176	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898177	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs898179	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs984116	0.85[EUR][1000 genomes]

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1233446	KLK7	cis	cerebellum	SCAN
rs1233446	KLK9	cis	parietal	SCAN
rs1233446	RUVBL2	cis	parietal	SCAN
rs1233446	SIGLEC16	cis	cerebellum	SCAN
rs1233446	GPR77	cis	cerebellum	SCAN
rs1233446	ZNF473	cis	cerebellum	SCAN
rs1233446	SYT3	cis	cerebellum	SCAN
rs1233446	SNORD33	cis	cerebellum	SCAN
rs1233446	FLT3LG	cis	parietal	SCAN
rs1233446	ZFP112	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:44729800-44768600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:44730000-44775600	ZNF genes & repeats	Liver	Liver
3	chr19:44742000-44763800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr19:44759600-44763800	Weak transcription	NH-A	brain
5	chr19:44760400-44763800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr19:44761400-44763800	Weak transcription	Esophagus	oesophagus
7	chr19:44761400-44764000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:44761800-44764000	Weak transcription	Fetal Brain Male	brain
9	chr19:44763200-44764400	Active TSS	Primary hematopoietic stem cells	blood
10	chr19:44763200-44764800	Active TSS	Rectal Mucosa Donor 31	rectum
11	chr19:44763400-44763800	Enhancers	NHDF-Ad	bronchial
12	chr19:44763400-44764000	Enhancers	Primary B cells from cord blood	blood
13	chr19:44763400-44764400	Active TSS	A549	lung
14	chr19:44763400-44764600	Active TSS	Brain Substantia Nigra	brain
15	chr19:44763400-44764600	Active TSS	Colon Smooth Muscle	Colon
16	chr19:44763400-44764800	Active TSS	Brain Angular Gyrus	brain
17	chr19:44763400-44765400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
18	chr19:44763600-44763800	Flanking Active TSS	Primary T cells from cord blood	blood
19	chr19:44763600-44763800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr19:44763600-44763800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
21	chr19:44763600-44763800	Enhancers	Fetal Thymus	thymus
22	chr19:44763600-44764000	Enhancers	Primary B cells from peripheral blood	blood
23	chr19:44763600-44764000	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:44763600-44764000	Enhancers	Placenta	Placenta
25	chr19:44763600-44764200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr19:44763600-44764200	Active TSS	Primary hematopoietic stem cells short term culture	blood
27	chr19:44763600-44764200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr19:44763600-44764200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr19:44763600-44764200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr19:44763600-44764200	Active TSS	Dnd41	blood
31	chr19:44763600-44764200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
32	chr19:44763600-44764200	Active TSS	NHEK	skin
33	chr19:44763600-44764400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:44763600-44764400	Active TSS	Cortex derived primary cultured neurospheres	brain
35	chr19:44763600-44764400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr19:44763600-44764400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr19:44763600-44764400	Active TSS	Fetal Brain Female	brain
38	chr19:44763600-44764600	Active TSS	Brain Germinal Matrix	brain
39	chr19:44763600-44764600	Active TSS	Fetal Intestine Large	intestine
40	chr19:44763600-44764600	Active TSS	Fetal Intestine Small	intestine
41	chr19:44763600-44764600	Active TSS	Fetal Lung	lung
42	chr19:44763600-44764800	Active TSS	ES-I3 Cell Line	embryonic stem cell
43	chr19:44763600-44764800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr19:44763600-44764800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:44763600-44764800	Active TSS	Right Ventricle	heart
46	chr19:44763600-44765000	Active TSS	HUES48 Cell Line	embryonic stem cell
47	chr19:44763600-44765000	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr19:44763600-44765000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr19:44763600-44765000	Active TSS	Brain Hippocampus Middle	brain
50	chr19:44763600-44765200	Active TSS	Duodenum Mucosa	Duodenum

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