Variant report

Variant	rs1353222
Chromosome Location	chr3:194799467-194799468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194792659..194796226-chr3:194797531..194801408,5	MCF-7	breast:
2	chr3:194798845..194800970-chr3:194805695..194807508,2	K562	blood:
3	chr3:194789447..194796347-chr3:194796697..194800807,6	K562	blood:
4	chr3:194784040..194786855-chr3:194798676..194802052,3	MCF-7	breast:
5	chr3:194797462..194799742-chr3:194801483..194805292,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10804419	1.00[ASW][hapmap];0.80[CEU][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.92[MEX][hapmap];0.84[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs10933695	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2642393	0.83[AFR][1000 genomes]
rs2720930	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.96[MEX][hapmap];0.95[MKK][hapmap];0.80[TSI][hapmap];0.89[YRI][hapmap]
rs2720949	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4677803	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6764788	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767698	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627506	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007697	chr3:194554814-195009930	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
2	nsv536873	chr3:194554814-195009930	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	28 gene(s)	inside rSNPs	diseases
3	nsv997779	chr3:194687093-194885936	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
4	nsv536874	chr3:194687093-194885936	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1009796	chr3:194737333-195124248	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	22 gene(s)	inside rSNPs	diseases
6	esv1813153	chr3:194754532-194851746	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv878136	chr3:194779412-194845226	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1353222	ATP13A5	cis	cerebellum	SCAN
rs1353222	C3orf43	cis	parietal	SCAN
rs1353222	LOC348840	cis	cerebellum	SCAN

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:194779000-194808000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr3:194780200-194800000	Weak transcription	Right Atrium	heart
3	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
4	chr3:194783600-194801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:194785600-194801400	Weak transcription	Fetal Lung	lung
6	chr3:194785600-194801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr3:194785600-194802000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:194786000-194800400	Weak transcription	GM12878-XiMat	blood
9	chr3:194787200-194800000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:194787600-194801000	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr3:194789800-194800000	Weak transcription	Primary hematopoietic stem cells	blood
12	chr3:194790400-194808000	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr3:194790600-194800000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:194790600-194800200	Weak transcription	Adipose Nuclei	Adipose
15	chr3:194790600-194800600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
16	chr3:194790600-194801000	Weak transcription	Brain Hippocampus Middle	brain
17	chr3:194790600-194801600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:194790600-194801800	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:194790600-194802000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:194790600-194802400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr3:194790600-194807800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr3:194790800-194799800	Weak transcription	Lung	lung
23	chr3:194790800-194800000	Weak transcription	HUVEC	blood vessel
24	chr3:194790800-194800400	Weak transcription	Fetal Brain Female	brain
25	chr3:194790800-194800600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:194790800-194800800	Weak transcription	Esophagus	oesophagus
27	chr3:194790800-194803600	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr3:194790800-194807400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:194790800-194807800	Weak transcription	HepG2	liver
30	chr3:194791000-194800400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:194791000-194801400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:194791600-194799800	Weak transcription	Hela-S3	cervix
34	chr3:194791600-194800200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:194792200-194800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr3:194792400-194804200	Enhancers	Fetal Thymus	thymus
37	chr3:194793600-194801200	Weak transcription	Stomach Smooth Muscle	stomach
38	chr3:194793800-194799800	Weak transcription	Left Ventricle	heart
39	chr3:194793800-194800600	Weak transcription	Primary T cells from cord blood	blood
40	chr3:194794000-194800600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr3:194794000-194807800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr3:194794800-194804400	Enhancers	Spleen	Spleen
43	chr3:194795400-194799600	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr3:194795400-194803800	Enhancers	Thymus	Thymus
45	chr3:194796000-194804000	Enhancers	Fetal Muscle Leg	muscle
46	chr3:194797000-194799800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr3:194797000-194799800	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr3:194797000-194800200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
49	chr3:194797200-194799600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:194797200-194801000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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