Variant report

Variant	rs6441225
Chromosome Location	chr3:158470321-158470322
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:158460949..158465729-chr3:158466898..158470534,5	K562	blood:
2	chr3:158439507..158442032-chr3:158469243..158472227,2	K562	blood:

Variant related genes	Relation type
ENSG00000118855	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1006911	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs1346834	0.88[ASN][1000 genomes]
rs1864508	0.88[ASN][1000 genomes]
rs2115941	0.88[ASN][1000 genomes]
rs2253249	0.90[JPT][hapmap]
rs2364927	0.93[ASN][1000 genomes]
rs2566346	0.81[ASN][1000 genomes]
rs2615052	0.89[ASN][1000 genomes]
rs4680460	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs4680467	0.86[ASN][1000 genomes]
rs57932243	0.94[ASN][1000 genomes]
rs6441224	0.91[ASN][1000 genomes]
rs6802315	0.89[ASN][1000 genomes]
rs7615751	0.89[ASN][1000 genomes]
rs7618110	0.90[ASN][1000 genomes]
rs7635993	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9822005	0.84[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs9861938	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9863103	0.85[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9881462	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6441225	LOC100287290	cis	cerebellar cortex	BrainEAC
rs6441225	RARRES1	cis	brain	BrainEAC

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:158449800-158483000	Weak transcription	Fetal Heart	heart
2	chr3:158450800-158485400	Weak transcription	Psoas Muscle	Psoas
3	chr3:158451000-158484200	Weak transcription	Rectal Smooth Muscle	rectum
4	chr3:158451000-158485800	Weak transcription	Fetal Kidney	kidney
5	chr3:158453600-158486400	Weak transcription	Esophagus	oesophagus
6	chr3:158457400-158486000	Weak transcription	Right Ventricle	heart
7	chr3:158457800-158486200	Weak transcription	Pancreas	Pancrea
8	chr3:158458000-158471200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:158460400-158486000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:158462800-158471200	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr3:158464400-158472600	Weak transcription	Colon Smooth Muscle	Colon
12	chr3:158465400-158480000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr3:158465800-158480200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr3:158466000-158472800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr3:158466000-158486000	Weak transcription	Aorta	Aorta
16	chr3:158466000-158486200	Weak transcription	Gastric	stomach
17	chr3:158466200-158482800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:158466200-158486200	Weak transcription	Brain Angular Gyrus	brain
19	chr3:158466200-158486200	Weak transcription	Fetal Brain Male	brain
20	chr3:158466600-158480000	Weak transcription	Fetal Brain Female	brain
21	chr3:158466600-158482600	Weak transcription	A549	lung
22	chr3:158466600-158485600	Weak transcription	Colonic Mucosa	Colon
23	chr3:158466600-158486200	Weak transcription	Brain Cingulate Gyrus	brain
24	chr3:158466800-158471600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:158466800-158473000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:158466800-158480200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:158466800-158480200	Weak transcription	Left Ventricle	heart
28	chr3:158466800-158486000	Weak transcription	Spleen	Spleen
29	chr3:158466800-158486200	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr3:158466800-158486200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:158467000-158483000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:158467600-158479000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr3:158467600-158480200	Weak transcription	Adipose Nuclei	Adipose
34	chr3:158467600-158485000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:158467600-158486000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr3:158467800-158480000	Weak transcription	Hela-S3	cervix
37	chr3:158468000-158470600	Weak transcription	K562	blood
38	chr3:158468000-158483600	Weak transcription	Stomach Smooth Muscle	stomach
39	chr3:158468000-158486200	Weak transcription	Lung	lung
40	chr3:158468200-158470600	Weak transcription	NHLF	lung
41	chr3:158468200-158488200	Weak transcription	Primary T cells from cord blood	blood
42	chr3:158468400-158477800	Weak transcription	Fetal Intestine Small	intestine
43	chr3:158468400-158483400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:158468600-158483200	Weak transcription	Fetal Stomach	stomach
45	chr3:158468600-158485000	Weak transcription	Fetal Intestine Large	intestine
46	chr3:158469000-158472800	Weak transcription	Fetal Lung	lung
47	chr3:158469400-158477200	Weak transcription	Osteobl	bone
48	chr3:158469800-158470800	Enhancers	HSMMtube	muscle
49	chr3:158470200-158477200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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