Variant report

Variant	rs3805486
Chromosome Location	chr5:40796045-40796046
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:40793843..40796817-chr5:40803354..40805786,3	K562	blood:
2	chr5:40753118..40757884-chr5:40795999..40799979,7	MCF-7	breast:
3	chr5:40755012..40759487-chr5:40796000..40799940,8	K562	blood:
4	chr5:40773088..40775822-chr5:40794513..40796616,2	MCF-7	breast:
5	chr5:40752834..40759871-chr5:40793841..40803866,19	K562	blood:
6	chr5:40795843..40803356-chr5:40833207..40837160,32	MCF-7	breast:

Variant related genes	Relation type
ENSG00000145592	Chromatin interaction
ENSG00000113638	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs16870224	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.80[TSI][hapmap]
rs16870378	0.84[ASW][hapmap];0.87[CHB][hapmap];0.96[CHD][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap]
rs3792822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4957341	0.94[CHB][hapmap];0.90[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881377	chr5:40753877-40810426	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
2	nsv881070	chr5:40753877-40827307	Enhancers Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv880438	chr5:40753877-40900717	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	160 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3805486	FBXO4	cis	parietal	SCAN
rs3805486	C7	cis	cerebellum	SCAN
rs3805486	PTGER4	cis	cerebellum	SCAN

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:40756200-40797200	Weak transcription	Gastric	stomach
2	chr5:40756400-40797400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr5:40765400-40796600	Weak transcription	Right Ventricle	heart
4	chr5:40765600-40796600	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr5:40776200-40797000	Weak transcription	Colonic Mucosa	Colon
6	chr5:40777000-40796600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr5:40777000-40796600	Weak transcription	Thymus	Thymus
8	chr5:40777000-40796800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr5:40777000-40797000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr5:40777200-40796600	Weak transcription	Fetal Thymus	thymus
11	chr5:40777200-40796800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr5:40777800-40796600	Weak transcription	NH-A	brain
13	chr5:40781000-40796800	Weak transcription	Aorta	Aorta
14	chr5:40788400-40796600	Weak transcription	Brain Anterior Caudate	brain
15	chr5:40788600-40796600	Weak transcription	Fetal Kidney	kidney
16	chr5:40788800-40796400	Weak transcription	Fetal Brain Female	brain
17	chr5:40788800-40796400	Weak transcription	Fetal Muscle Leg	muscle
18	chr5:40788800-40796600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:40788800-40796600	Weak transcription	Fetal Stomach	stomach
20	chr5:40788800-40797400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr5:40789000-40796600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:40789200-40796600	Weak transcription	Brain Germinal Matrix	brain
23	chr5:40789600-40796600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr5:40789800-40796800	Weak transcription	Fetal Heart	heart
25	chr5:40790400-40797200	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr5:40790600-40797200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:40791800-40796400	Weak transcription	NHEK	skin
28	chr5:40791800-40796600	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:40792000-40796400	Weak transcription	HMEC	breast
30	chr5:40792000-40796600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr5:40792000-40796600	Weak transcription	Right Atrium	heart
32	chr5:40792000-40796600	Weak transcription	HSMMtube	muscle
33	chr5:40792200-40796400	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr5:40792400-40796400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr5:40792400-40796600	Weak transcription	Pancreatic Islets	Pancreatic Islet
36	chr5:40792400-40796800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr5:40792600-40796600	Weak transcription	Colon Smooth Muscle	Colon
38	chr5:40793000-40796400	Enhancers	HepG2	liver
39	chr5:40793600-40796400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr5:40793600-40796800	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr5:40793800-40797000	Weak transcription	Brain Substantia Nigra	brain
42	chr5:40794000-40796400	Weak transcription	Primary T cells from cord blood	blood
43	chr5:40794000-40796400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:40794200-40797200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr5:40794400-40796200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr5:40795200-40796200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr5:40795200-40796200	Strong transcription	Fetal Muscle Trunk	muscle
48	chr5:40795200-40796400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
49	chr5:40795200-40796600	Enhancers	Sigmoid Colon	Sigmoid Colon
50	chr5:40795200-40796600	Enhancers	Small Intestine	intestine

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