Variant report

Variant	rs12493280
Chromosome Location	chr3:158529117-158529118
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:158528525..158531517-chr3:158531564..158533264,2	K562	blood:
2	chr3:158527065..158529292-chr3:158543447..158545685,2	K562	blood:
3	chr3:158519720..158521508-chr3:158527102..158529804,2	MCF-7	breast:
4	chr3:158519080..158523533-chr3:158523571..158529220,8	MCF-7	breast:
5	chr10:128997126..128997953-chr3:158528435..158529327,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118855	Chromatin interaction
ENSG00000272247	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10936160	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10936162	0.86[LWK][hapmap];0.80[AFR][1000 genomes]
rs12497958	0.81[AFR][1000 genomes]
rs12638831	0.98[ASN][1000 genomes]
rs1381463	0.98[ASN][1000 genomes]
rs2244996	0.88[ASN][1000 genomes]
rs2364921	0.85[ASN][1000 genomes]
rs2713736	0.88[ASN][1000 genomes]
rs61796775	0.82[AFR][1000 genomes]
rs6778714	0.82[JPT][hapmap]
rs6802844	0.85[ASN][1000 genomes]
rs7429205	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs751834	0.82[JPT][hapmap]
rs9861042	1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002378	chr3:157715428-158673414	Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv1004124	chr3:158146715-158808638	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv530059	chr3:158332590-159147549	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
4	nsv1014255	chr3:158358860-158768542	Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv532665	chr3:158370013-158754245	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv948755	chr3:158388780-158672287	Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
7	nsv877692	chr3:158430706-158828643	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
8	nsv1001450	chr3:158440011-158768399	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
9	nsv536777	chr3:158440011-158768399	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv877693	chr3:158470321-158583004	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
11	nsv1006146	chr3:158475824-158625778	Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
12	nsv592123	chr3:158477796-158625128	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
13	nsv1002514	chr3:158484027-158673414	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
14	nsv536778	chr3:158484027-158673414	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
15	nsv1014511	chr3:158516495-158715240	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12493280	TIPARP	cis	cerebellum	SCAN
rs12493280	LXN	cis	cerebellum	SCAN
rs12493280	RARRES1	cis	frontal cortex	BrainEAC

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158520400-158552400	Weak transcription	Stomach Mucosa	stomach
2	chr3:158520600-158543400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:158520800-158545400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr3:158521000-158543200	Weak transcription	HUES6 Cell Line	embryonic stem cell
5	chr3:158521400-158544400	Weak transcription	HepG2	liver
6	chr3:158522200-158533200	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr3:158522400-158550000	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:158522600-158533200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr3:158522600-158533600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:158522800-158532400	Weak transcription	A549	lung
11	chr3:158522800-158533400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:158523000-158533200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr3:158523000-158544000	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr3:158523400-158533200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:158523400-158533200	Strong transcription	Primary T helper cells PMA-I stimulated	--
16	chr3:158523400-158533200	Strong transcription	Liver	Liver
17	chr3:158523600-158533200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:158523600-158533200	Strong transcription	Skeletal Muscle Male	skeletal muscle
19	chr3:158524000-158529400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:158524600-158533200	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr3:158524800-158533200	Strong transcription	Brain Anterior Caudate	brain
22	chr3:158525200-158533200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:158525200-158533200	Strong transcription	Duodenum Mucosa	Duodenum
24	chr3:158525400-158529400	Strong transcription	Brain Angular Gyrus	brain
25	chr3:158525400-158530400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr3:158525400-158530600	Strong transcription	Fetal Lung	lung
27	chr3:158525400-158530800	Strong transcription	Lung	lung
28	chr3:158525400-158530800	Strong transcription	Stomach Smooth Muscle	stomach
29	chr3:158525400-158532000	Strong transcription	Brain Hippocampus Middle	brain
30	chr3:158525400-158533200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr3:158525400-158533200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr3:158525400-158533200	Strong transcription	Adipose Nuclei	Adipose
33	chr3:158525400-158533200	Strong transcription	Fetal Intestine Large	intestine
34	chr3:158525400-158533200	Strong transcription	Placenta	Placenta
35	chr3:158525400-158533200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr3:158525600-158529600	Strong transcription	Left Ventricle	heart
37	chr3:158525600-158530800	Strong transcription	Aorta	Aorta
38	chr3:158525600-158530800	Strong transcription	Fetal Muscle Trunk	muscle
39	chr3:158525600-158530800	Strong transcription	Rectal Smooth Muscle	rectum
40	chr3:158525600-158531000	Strong transcription	Gastric	stomach
41	chr3:158525600-158531200	Strong transcription	Spleen	Spleen
42	chr3:158525600-158531800	Strong transcription	Brain Substantia Nigra	brain
43	chr3:158525600-158532800	Strong transcription	Ovary	ovary
44	chr3:158525600-158533200	Strong transcription	Brain Inferior Temporal Lobe	brain
45	chr3:158525600-158533200	Strong transcription	Colon Smooth Muscle	Colon
46	chr3:158525600-158533200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:158525600-158533200	Strong transcription	Fetal Muscle Leg	muscle
48	chr3:158525600-158533200	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:158525800-158531400	Strong transcription	Small Intestine	intestine
50	chr3:158525800-158532000	Strong transcription	Colonic Mucosa	Colon

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