Variant report

Variant	rs299192
Chromosome Location	chr5:118315744-118315745
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:118311467..118314093-chr5:118314485..118317147,2	K562	blood:

Extended variants
information (count: 20 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10900727	1.00[JPT][hapmap]
rs11959589	0.83[YRI][hapmap]
rs4286709	1.00[JPT][hapmap]
rs4380699	1.00[JPT][hapmap]
rs4583917	1.00[JPT][hapmap]
rs4895185	1.00[JPT][hapmap]
rs6595174	1.00[JPT][hapmap]
rs6880622	1.00[JPT][hapmap]
rs6889308	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6893733	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6894429	0.96[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6894997	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7734532	1.00[JPT][hapmap]
rs7736400	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9327087	1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv882767	chr5:117931730-118385691	Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1017548	chr5:118276479-118358394	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1015878	chr5:118288904-118414706	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv537881	chr5:118288904-118414706	Active TSS Genic enhancers Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	nsv964930	chr5:118301974-118317943	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs299192	SNCAIP	cis	parietal	SCAN
rs299192	DTWD2	cis	parietal	SCAN
rs299192	ANXA1	trans	lymphoblastoid	seeQTL

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:118304600-118321600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
2	chr5:118305200-118320400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:118305200-118322400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr5:118309600-118323000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr5:118310800-118320800	Weak transcription	Hela-S3	cervix
6	chr5:118311400-118316000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr5:118311400-118322800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr5:118313000-118323000	Weak transcription	Fetal Heart	heart
9	chr5:118313600-118322200	Weak transcription	Primary B cells from cord blood	blood
10	chr5:118314000-118322400	Weak transcription	Primary T cells from cord blood	blood
11	chr5:118314600-118316000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:118314600-118316000	Weak transcription	Gastric	stomach
13	chr5:118314600-118322400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr5:118314600-118323000	Weak transcription	Brain Angular Gyrus	brain
15	chr5:118314600-118323400	Weak transcription	Aorta	Aorta
16	chr5:118315000-118316200	Strong transcription	Primary hematopoietic stem cells	blood
17	chr5:118315200-118316400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:118315400-118316200	Strong transcription	Ovary	ovary
19	chr5:118315600-118316000	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
20	chr5:118315600-118316400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr5:118315600-118316400	Enhancers	HepG2	liver
22	chr5:118315600-118322800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr5:118315600-118322800	Weak transcription	Brain Hippocampus Middle	brain

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