Variant report

Variant	rs1483185
Chromosome Location	chr3:53199014-53199015
allele	G/T
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	NR3C1	chr3:53198777-53199057	A549	lung:	n/a	chr3:53198890-53198911 chr3:53198891-53198909 chr3:53198893-53198907 chr3:53198892-53198908 chr3:53198887-53198913 chr3:53198892-53198908 chr3:53198892-53198908 chr3:53198893-53198907 chr3:53198892-53198908 chr3:53198889-53198910
2	POLR2A	chr3:53198575-53202827	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:53198677-53200845	GM12878	blood:	n/a	n/a
4	STAT5A	chr3:53198559-53199777	GM12878	blood:	n/a	chr3:53199425-53199433 chr3:53198974-53198985
5	POLR2A	chr3:53198817-53199562	GM12878	blood:	n/a	n/a
6	NR3C1	chr3:53198632-53199132	A549	lung:	n/a	chr3:53198890-53198911 chr3:53198891-53198909 chr3:53198893-53198907 chr3:53198892-53198908 chr3:53198887-53198913 chr3:53198892-53198908 chr3:53198892-53198908 chr3:53198893-53198907 chr3:53198892-53198908 chr3:53198889-53198910
7	NR3C1	chr3:53198612-53199108	A549	lung:	n/a	chr3:53198890-53198911 chr3:53198891-53198909 chr3:53198893-53198907 chr3:53198892-53198908 chr3:53198887-53198913 chr3:53198892-53198908 chr3:53198892-53198908 chr3:53198893-53198907 chr3:53198892-53198908 chr3:53198889-53198910
8	POLR2A	chr3:53198952-53199254	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:53198960-53199349	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:53188104..53190681-chr3:53198828..53201211,3	K562	blood:
2	chr3:53196507..53199069-chr3:53217529..53219666,3	K562	blood:
3	chr3:53197947..53200890-chr3:53261082..53263674,2	K562	blood:

Variant related genes	Relation type
PRKCD	TF binding region
ENSG00000163931	Chromatin interaction
ENSG00000163932	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11130344	0.80[CHD][hapmap]
rs11130347	0.81[ASN][1000 genomes]
rs11924565	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs1483186	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs1483187	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2242305	0.82[ASN][1000 genomes]
rs2306571	0.90[JPT][hapmap]
rs3773724	0.90[ASN][1000 genomes]
rs3773726	0.91[CHB][hapmap];0.90[JPT][hapmap];0.90[ASN][1000 genomes]
rs3773727	0.91[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3773729	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs3773731	0.88[ASN][1000 genomes]
rs3773733	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3821689	0.81[JPT][hapmap]
rs57046386	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs62254282	0.82[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs6775022	0.90[ASN][1000 genomes]
rs6778964	0.84[CHD][hapmap];0.81[JPT][hapmap]
rs6797662	0.90[ASN][1000 genomes]
rs6807359	0.90[CHD][hapmap]
rs72537447	0.83[ASN][1000 genomes]
rs7630325	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834699	chr3:53151876-53325808	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	nsv517233	chr3:53175557-53321002	Transcr. at gene 5' and 3' Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1483185	SPATA12	cis	parietal	SCAN
rs1483185	DUSP7	cis	cerebellum	SCAN
rs1483185	TLR9	cis	parietal	SCAN
rs1483185	MUSTN1	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:53196400-53199200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr3:53196400-53202000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:53196400-53210200	Weak transcription	Psoas Muscle	Psoas
4	chr3:53196400-53212400	Weak transcription	Aorta	Aorta
5	chr3:53196600-53199800	Weak transcription	Brain Germinal Matrix	brain
6	chr3:53196600-53200000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:53196600-53204000	Weak transcription	Small Intestine	intestine
8	chr3:53196800-53199400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr3:53197000-53200400	Weak transcription	Liver	Liver
10	chr3:53197000-53200400	Weak transcription	HSMMtube	muscle
11	chr3:53197000-53202000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:53197200-53199800	Weak transcription	NH-A	brain
13	chr3:53197200-53200200	Weak transcription	HUVEC	blood vessel
14	chr3:53197200-53200400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr3:53197200-53200400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:53197200-53200400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr3:53197200-53200400	Weak transcription	Brain Angular Gyrus	brain
18	chr3:53197200-53200400	Weak transcription	HSMM	muscle
19	chr3:53197200-53200600	Weak transcription	Fetal Kidney	kidney
20	chr3:53197200-53200800	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:53197200-53201800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:53197200-53205400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:53197200-53213400	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr3:53197400-53199200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:53197400-53199200	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:53197400-53199600	Enhancers	HMEC	breast
27	chr3:53197400-53199800	Weak transcription	Placenta	Placenta
28	chr3:53197400-53199800	Weak transcription	Right Atrium	heart
29	chr3:53197400-53199800	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:53197400-53199800	Weak transcription	Stomach Smooth Muscle	stomach
31	chr3:53197400-53200000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr3:53197400-53200200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:53197400-53200400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:53197400-53200400	Weak transcription	Ovary	ovary
35	chr3:53197400-53200600	Weak transcription	Brain Cingulate Gyrus	brain
36	chr3:53197400-53200800	Weak transcription	H1 Cell Line	embryonic stem cell
37	chr3:53197400-53200800	Weak transcription	Rectal Smooth Muscle	rectum
38	chr3:53197400-53202000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr3:53197400-53202200	Weak transcription	Brain Substantia Nigra	brain
40	chr3:53197400-53203000	Genic enhancers	Primary B cells from peripheral blood	blood
41	chr3:53197400-53207000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr3:53197600-53199200	Weak transcription	Right Ventricle	heart
43	chr3:53197600-53199400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
44	chr3:53197600-53199600	Enhancers	Primary B cells from cord blood	blood
45	chr3:53197600-53199800	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:53197600-53200200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr3:53197600-53200400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr3:53197600-53200400	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr3:53197600-53200400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr3:53197600-53201000	Weak transcription	HepG2	liver

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