Variant report

Variant	rs7627506
Chromosome Location	chr3:194804838-194804839
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:194778538..194781449-chr3:194803354..194805108,2	K562	blood:
2	chr3:194797462..194799742-chr3:194801483..194805292,3	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs10804419	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]
rs10933695	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1353222	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]
rs2642393	0.84[AFR][1000 genomes]
rs2720930	1.00[CHB][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap]
rs2720949	0.91[CEU][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4677803	1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6764788	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6767698	0.91[AMR][1000 genomes];0.93[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs7627506	ATP13A5	cis	cerebellum	SCAN
rs7627506	C3orf43	cis	parietal	SCAN
rs7627506	LOC348840	cis	cerebellum	SCAN
rs7627506	DLG1	cis	cerebellum	SCAN

Chromatin state (count:63 , 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	chr3:194790800-194807400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
6	chr3:194790800-194807800	Weak transcription	HepG2	liver
7	chr3:194791000-194821800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr3:194794000-194807800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr3:194797200-194808200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:194799400-194807000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr3:194801000-194807800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr3:194801000-194814600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr3:194801200-194806400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:194801200-194808200	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:194801200-194814800	Weak transcription	Primary T cells from cord blood	blood
16	chr3:194801200-194814800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr3:194801400-194806800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:194801600-194806600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:194801600-194808400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr3:194801800-194807400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:194802000-194826800	Weak transcription	Brain Cingulate Gyrus	brain
22	chr3:194802600-194807400	Weak transcription	K562	blood
23	chr3:194802600-194807800	Weak transcription	Fetal Lung	lung
24	chr3:194802800-194805200	Weak transcription	Fetal Intestine Small	intestine
25	chr3:194802800-194807200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr3:194803000-194806000	Weak transcription	Fetal Stomach	stomach
27	chr3:194803000-194807200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr3:194803000-194807600	Weak transcription	Esophagus	oesophagus
29	chr3:194803000-194814400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr3:194803200-194807200	Weak transcription	Pancreas	Pancrea
31	chr3:194803200-194808000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr3:194803200-194815800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr3:194803600-194808000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr3:194803800-194805200	Weak transcription	Right Atrium	heart
35	chr3:194803800-194805400	Weak transcription	Adipose Nuclei	Adipose
36	chr3:194803800-194805800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr3:194803800-194806200	Weak transcription	Thymus	Thymus
38	chr3:194803800-194807400	Weak transcription	Left Ventricle	heart
39	chr3:194803800-194807600	Weak transcription	Lung	lung
40	chr3:194803800-194807600	Weak transcription	Stomach Mucosa	stomach
41	chr3:194803800-194807800	Weak transcription	Placenta	Placenta
42	chr3:194804000-194805400	Weak transcription	Fetal Muscle Leg	muscle
43	chr3:194804000-194807000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr3:194804000-194807400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr3:194804000-194807800	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:194804000-194807800	Weak transcription	Gastric	stomach
47	chr3:194804000-194818200	Weak transcription	Right Ventricle	heart
48	chr3:194804200-194805400	Weak transcription	Fetal Thymus	thymus
49	chr3:194804200-194806800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr3:194804200-194807000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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