Variant report

Variant	rs1807403
Chromosome Location	chr3:43102291-43102292
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	chr3:43101835..43104302-chr3:43113340..43115119,2	K562	blood:

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs2280565	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs2936817	0.82[CHD][hapmap]
rs34970115	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs3732858	0.82[MKK][hapmap]
rs473467	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs504973	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs536119	0.81[CHB][hapmap];0.92[CHD][hapmap];0.82[JPT][hapmap];0.83[MEX][hapmap]
rs658958	0.82[CHD][hapmap]
rs660446	0.81[CHB][hapmap];0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460522	chr3:42967597-43175207	Weak transcription Active TSS Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv590149	chr3:42967597-43175207	Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1807403	C3orf39	cis	cerebellum	SCAN
rs1807403	C3orf39	cis	parietal	SCAN
rs1807403	ZNF662	cis	parietal	SCAN
rs1807403	CCDC13	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:43092800-43117800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr3:43093400-43120200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr3:43094200-43104200	Weak transcription	Gastric	stomach
4	chr3:43094400-43114800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:43095000-43114800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:43095800-43104400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:43096200-43121200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:43096800-43102600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr3:43097200-43104600	Weak transcription	Brain Substantia Nigra	brain
10	chr3:43098800-43104200	Weak transcription	Ovary	ovary
11	chr3:43100200-43120200	Weak transcription	Brain Angular Gyrus	brain
12	chr3:43101000-43102400	Strong transcription	Liver	Liver
13	chr3:43101000-43102600	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:43101000-43102800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
15	chr3:43101000-43105000	Enhancers	Fetal Thymus	thymus
16	chr3:43101200-43102800	Enhancers	Primary T cells from cord blood	blood
17	chr3:43101200-43102800	Enhancers	Primary T helper cells PMA-I stimulated	--
18	chr3:43101200-43103200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:43101200-43103200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
20	chr3:43101400-43102400	Weak transcription	Rectal Mucosa Donor 29	rectum
21	chr3:43101400-43102600	Enhancers	Thymus	Thymus
22	chr3:43101400-43102800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr3:43101400-43102800	Strong transcription	Brain Hippocampus Middle	brain
24	chr3:43101600-43102600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr3:43101600-43102600	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr3:43101600-43121000	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr3:43101800-43103200	Enhancers	Primary T cells fromperipheralblood	blood
28	chr3:43101800-43103200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr3:43101800-43105000	ZNF genes & repeats	Fetal Stomach	stomach
30	chr3:43102000-43103200	Weak transcription	Right Atrium	heart
31	chr3:43102000-43104000	Weak transcription	Placenta	Placenta
32	chr3:43102000-43121000	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr3:43102200-43102400	Weak transcription	Stomach Smooth Muscle	stomach
34	chr3:43102200-43103000	Enhancers	Fetal Muscle Leg	muscle

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