Variant report

Variant	rs10804419
Chromosome Location	chr3:194807735-194807736
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10933695	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs1353222	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]
rs2720930	0.84[GIH][hapmap];0.87[MEX][hapmap];0.89[YRI][hapmap]
rs4677661	1.00[CHB][hapmap]
rs4677803	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6764788	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6767698	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs7627506	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9288754	1.00[CHB][hapmap]
rs9825174	1.00[CHB][hapmap]
rs9827336	0.84[AMR][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
rs10804419	LOC348840	cis	cerebellum	SCAN
rs10804419	ATP13A5	cis	cerebellum	SCAN
rs10804419	C3orf43	cis	parietal	SCAN

Chromatin state (count:61 , 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	chr3:194781000-194808000	Weak transcription	Colonic Mucosa	Colon
3	chr3:194790400-194808000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr3:194790600-194807800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:194790800-194807800	Weak transcription	HepG2	liver
6	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr3:194794000-194807800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr3:194797200-194808200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr3:194801000-194807800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr3:194801000-194814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr3:194801200-194808200	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:194801200-194814800	Weak transcription	Primary T cells from cord blood	blood
13	chr3:194801200-194814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr3:194801600-194808400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:194802600-194807800	Weak transcription	Fetal Lung	lung
17	chr3:194803000-194814400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr3:194803200-194808000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr3:194803200-194815800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr3:194803600-194808000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr3:194803800-194807800	Weak transcription	Placenta	Placenta
22	chr3:194804000-194807800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr3:194804000-194807800	Weak transcription	Gastric	stomach
24	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
25	chr3:194805400-194809200	Enhancers	Fetal Thymus	thymus
26	chr3:194805800-194807800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr3:194806000-194807800	Weak transcription	Adipose Nuclei	Adipose
28	chr3:194806000-194807800	Strong transcription	Fetal Stomach	stomach
29	chr3:194806200-194808000	Weak transcription	Fetal Muscle Leg	muscle
30	chr3:194806600-194807800	Weak transcription	Fetal Intestine Small	intestine
31	chr3:194806600-194808200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:194806600-194808200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr3:194806600-194808800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr3:194806800-194808000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:194806800-194808400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
36	chr3:194806800-194808400	Enhancers	Thymus	Thymus
37	chr3:194806800-194808800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr3:194806800-194826400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr3:194807000-194808000	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr3:194807000-194808400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr3:194807000-194808400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr3:194807000-194808800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:194807200-194807800	Enhancers	Spleen	Spleen
44	chr3:194807200-194808000	Enhancers	H1 Cell Line	embryonic stem cell
45	chr3:194807200-194808000	Enhancers	HUES48 Cell Line	embryonic stem cell
46	chr3:194807200-194808000	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:194807200-194808000	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr3:194807200-194808000	Enhancers	Breast Myoepithelial Primary Cells	Breast
49	chr3:194807200-194808200	Enhancers	ES-I3 Cell Line	embryonic stem cell
50	chr3:194807200-194808400	Enhancers	Pancreas	Pancrea

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