Variant report

Variant	rs2720930
Chromosome Location	chr3:194789032-194789033
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:194787100..194789938-chr3:194793885..194796418,2	K562	blood:
2	chr3:194624572..194626596-chr3:194788748..194791365,2	K562	blood:
3	chr3:194405223..194406837-chr3:194788272..194790538,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000185112	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs10804419	0.84[GIH][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap]
rs1353222	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	0.80[EUR][1000 genomes]
rs7627506	1.00[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948797	chr3:194232753-194789163	Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
8	esv1847174	chr3:194763601-194792415	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	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
10	esv3321941	chr3:194784663-194789461	Strong transcription Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	esv1848714	chr3:194785443-194792415	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv819035	chr3:194786039-194789122	Weak transcription Strong transcription Enhancers ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv822407	chr3:194786273-194789043	Weak transcription Strong transcription ZNF genes & repeats Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2720930	ATP13A5	cis	cerebellum	SCAN
rs2720930	DLG1	cis	cerebellum	SCAN
rs2720930	LOC348840	cis	cerebellum	SCAN

Chromatin state (count:100 , 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	chr3:194781000-194789400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
5	chr3:194782000-194790000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:194783400-194789800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr3:194783600-194801400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:194784000-194797800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:194784200-194789600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:194784200-194790200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr3:194784200-194797400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:194785200-194789800	Weak transcription	Aorta	Aorta
13	chr3:194785200-194796600	Weak transcription	NHLF	lung
14	chr3:194785400-194790200	Weak transcription	Esophagus	oesophagus
15	chr3:194785400-194793400	Weak transcription	Left Ventricle	heart
16	chr3:194785400-194799200	Weak transcription	Pancreas	Pancrea
17	chr3:194785600-194789600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:194785600-194790000	Weak transcription	Colon Smooth Muscle	Colon
19	chr3:194785600-194791000	Weak transcription	Small Intestine	intestine
20	chr3:194785600-194792400	Weak transcription	Right Ventricle	heart
21	chr3:194785600-194801400	Weak transcription	Fetal Lung	lung
22	chr3:194785600-194801600	Weak transcription	Duodenum Smooth Muscle	Duodenum
23	chr3:194785600-194802000	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:194785800-194789400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr3:194786000-194789200	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr3:194786000-194789400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr3:194786000-194789400	Weak transcription	HepG2	liver
28	chr3:194786000-194790600	Weak transcription	Stomach Mucosa	stomach
29	chr3:194786000-194791000	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr3:194786000-194791000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:194786000-194796600	Weak transcription	Primary B cells from cord blood	blood
32	chr3:194786000-194800400	Weak transcription	GM12878-XiMat	blood
33	chr3:194786200-194789600	Weak transcription	Spleen	Spleen
34	chr3:194786600-194789600	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:194786800-194790600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr3:194786800-194791000	Weak transcription	Osteobl	bone
37	chr3:194787000-194789800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:194787200-194789600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr3:194787200-194789800	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr3:194787200-194800000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr3:194787400-194789800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr3:194787400-194790000	Weak transcription	Brain Anterior Caudate	brain
43	chr3:194787400-194791000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr3:194787400-194791600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:194787400-194793800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
46	chr3:194787400-194795200	Strong transcription	Fetal Stomach	stomach
47	chr3:194787600-194789400	Weak transcription	Thymus	Thymus
48	chr3:194787600-194789600	Weak transcription	Ovary	ovary
49	chr3:194787600-194789800	Weak transcription	Brain Germinal Matrix	brain
50	chr3:194787600-194790600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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