Variant report

Variant	rs3209874
Chromosome Location	chr5:112358890-112358891
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10059132	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10065319	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10076751	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10463645	0.95[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10515453	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[CHD][hapmap];0.90[GIH][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13360862	0.87[ASW][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs1422222	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1978430	0.89[EUR][1000 genomes]
rs2080898	0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[MEX][hapmap];0.82[TSI][hapmap]
rs2080899	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs3733968	1.00[CEU][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.88[EUR][1000 genomes]
rs4309965	0.82[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs58280144	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594654	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6594655	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6594656	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6594661	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6865320	0.80[JPT][hapmap]
rs6876686	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6888851	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6888965	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6892784	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7033	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7733267	0.90[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9326868	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv599394	chr5:112185491-112446323	Weak transcription Active TSS Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv882717	chr5:112336588-112408944	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3209874	TSLP	cis	parietal	SCAN
rs3209874	MCC	cis	cerebellum	SCAN
rs3209874	DCP2	cis	parietal	SCAN
rs3209874	AQPEP	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112314200-112362600	Weak transcription	Colonic Mucosa	Colon
2	chr5:112315600-112362600	Weak transcription	Brain Angular Gyrus	brain
3	chr5:112317800-112366200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr5:112318400-112365600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr5:112319800-112363800	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr5:112320000-112364200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr5:112320600-112362600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:112321200-112364800	Strong transcription	HUES64 Cell Line	embryonic stem cell
9	chr5:112321400-112363800	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr5:112322600-112362400	Weak transcription	Psoas Muscle	Psoas
11	chr5:112322800-112362400	Weak transcription	Esophagus	oesophagus
12	chr5:112324800-112369800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr5:112327800-112364600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr5:112330200-112362800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:112332400-112372600	Weak transcription	Fetal Brain Male	brain
16	chr5:112333000-112359800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:112333200-112362400	Weak transcription	Right Ventricle	heart
18	chr5:112334000-112365200	Strong transcription	Placenta	Placenta
19	chr5:112338600-112360800	Weak transcription	Aorta	Aorta
20	chr5:112339200-112362400	Weak transcription	Pancreas	Pancrea
21	chr5:112339400-112362000	Weak transcription	Gastric	stomach
22	chr5:112340400-112362400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr5:112340400-112362600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr5:112340400-112362600	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr5:112342200-112362600	Weak transcription	Brain Inferior Temporal Lobe	brain
26	chr5:112349800-112359600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:112349800-112362400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr5:112349800-112366600	Weak transcription	Colon Smooth Muscle	Colon
29	chr5:112350000-112360600	Weak transcription	Fetal Intestine Small	intestine
30	chr5:112350200-112361400	Weak transcription	Brain Substantia Nigra	brain
31	chr5:112350200-112361400	Weak transcription	Lung	lung
32	chr5:112350200-112361400	Weak transcription	Ovary	ovary
33	chr5:112350200-112362000	Weak transcription	Placenta Amnion	Placenta Amnion
34	chr5:112350200-112362600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr5:112350200-112362600	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr5:112350200-112362600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:112350200-112362600	Weak transcription	Brain Anterior Caudate	brain
38	chr5:112350200-112362800	Weak transcription	Brain Cingulate Gyrus	brain
39	chr5:112350400-112359800	Weak transcription	Left Ventricle	heart
40	chr5:112350400-112360800	Weak transcription	Fetal Intestine Large	intestine
41	chr5:112350400-112361000	Weak transcription	Fetal Stomach	stomach
42	chr5:112350400-112361400	Weak transcription	Stomach Smooth Muscle	stomach
43	chr5:112350400-112361800	Weak transcription	Brain Hippocampus Middle	brain
44	chr5:112350400-112362000	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr5:112350400-112362400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr5:112350400-112362400	Weak transcription	Spleen	Spleen
47	chr5:112350400-112362600	Weak transcription	Fetal Brain Female	brain
48	chr5:112350400-112362600	Weak transcription	Rectal Smooth Muscle	rectum
49	chr5:112350400-112362600	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr5:112350600-112362400	Weak transcription	Brain Germinal Matrix	brain

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