Variant report

Variant	rs9838301
Chromosome Location	chr3:121375144-121375145
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 43 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10049060	1.00[CEU][hapmap];0.94[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1127412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1128163	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11916169	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12496318	1.00[CEU][hapmap]
rs12634032	1.00[CEU][hapmap]
rs12635865	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1463736	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1574115	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1574133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2141487	1.00[CEU][hapmap]
rs3732407	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3732410	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3772126	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4048699	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4048703	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58367397	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6771068	1.00[CEU][hapmap]
rs6791882	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7153	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610298	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7623901	1.00[CEU][hapmap]
rs7637495	1.00[CEU][hapmap]
rs7647351	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648340	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7648343	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9808981	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9817818	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9818073	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9820511	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824235	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9824760	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9850439	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9852845	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9874722	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv591395	chr3:120970900-121501070	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv591396	chr3:120970900-121557533	Strong transcription Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv591397	chr3:120977383-121505882	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
4	nsv999335	chr3:121100283-121408766	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Enhancers 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	18 gene(s)	inside rSNPs	diseases
5	nsv998740	chr3:121289499-121390271	Strong transcription Weak transcription Genic enhancers Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv432480	chr3:121355723-121629928	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
7	nsv432482	chr3:121364236-121629634	Weak transcription ZNF genes & repeats Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
8	nsv432481	chr3:121364236-121637178	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9838301	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs9838301	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs9838301	IQCB1	Cis_1M	lymphoblastoid	RTeQTL
rs9838301	EAF2	cis	multi-tissue	Pritchard
rs9838301	STAM2	trans	lymphoblastoid	RTeQTL

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121345600-121376800	Weak transcription	Esophagus	oesophagus
2	chr3:121347000-121378000	Weak transcription	Right Ventricle	heart
3	chr3:121348000-121381800	Weak transcription	Aorta	Aorta
4	chr3:121349000-121378000	Weak transcription	Fetal Stomach	stomach
5	chr3:121351000-121382800	Weak transcription	Small Intestine	intestine
6	chr3:121351400-121381400	Weak transcription	Gastric	stomach
7	chr3:121353400-121376000	Weak transcription	Lung	lung
8	chr3:121354000-121381000	Weak transcription	Fetal Intestine Small	intestine
9	chr3:121356200-121378200	Weak transcription	Colonic Mucosa	Colon
10	chr3:121356800-121379200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr3:121362200-121379400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr3:121362600-121379600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr3:121364000-121377000	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr3:121364200-121375800	Weak transcription	Spleen	Spleen
15	chr3:121364200-121377000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:121364200-121378200	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr3:121364200-121378800	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:121367400-121379000	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:121367400-121381800	Weak transcription	Pancreas	Pancrea
20	chr3:121367600-121377600	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:121367600-121378000	Weak transcription	Fetal Muscle Leg	muscle
22	chr3:121367600-121378200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:121367600-121378800	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:121367800-121378800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:121368400-121377600	Weak transcription	Left Ventricle	heart
26	chr3:121368800-121380000	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:121369400-121376200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:121369800-121377600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:121370600-121379400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr3:121370600-121381600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:121371000-121383600	Weak transcription	Hela-S3	cervix
32	chr3:121371400-121378200	Weak transcription	Brain Anterior Caudate	brain
33	chr3:121371600-121376200	Strong transcription	Placenta	Placenta
34	chr3:121371800-121378000	Genic enhancers	Primary T helper cells fromperipheralblood	blood
35	chr3:121372400-121376600	Strong transcription	Liver	Liver
36	chr3:121372400-121377800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr3:121372600-121379000	Weak transcription	Fetal Heart	heart
38	chr3:121373000-121380400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr3:121373200-121377600	Genic enhancers	Dnd41	blood
40	chr3:121373800-121377800	Weak transcription	HUVEC	blood vessel
41	chr3:121374000-121376000	Weak transcription	Thymus	Thymus
42	chr3:121374000-121376800	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr3:121374000-121376800	Strong transcription	Fetal Thymus	thymus
44	chr3:121374000-121376800	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr3:121374000-121377400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr3:121374000-121377600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr3:121374000-121379600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr3:121374200-121376000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:121374200-121376200	Strong transcription	Primary B cells from peripheral blood	blood
50	chr3:121374200-121377000	Strong transcription	Primary B cells from cord blood	blood

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