Variant report

Variant	rs9855306
Chromosome Location	chr3:138215114-138215115
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:86)

rs_ID	r²[population]
rs1082034	0.92[ASN][1000 genomes]
rs10935282	0.95[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs10935284	0.82[EUR][1000 genomes]
rs10935287	0.87[ASN][1000 genomes]
rs11709290	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11717771	0.88[ASN][1000 genomes]
rs11916525	0.82[JPT][hapmap]
rs12487652	0.86[ASN][1000 genomes]
rs12487694	0.92[ASN][1000 genomes]
rs12490633	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs12497070	0.86[ASN][1000 genomes]
rs12630060	0.82[JPT][hapmap]
rs12632794	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs12635490	0.86[JPT][hapmap]
rs12635904	0.82[JPT][hapmap]
rs12636246	0.86[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]
rs12636910	0.95[CHB][hapmap];0.97[CHD][hapmap];0.81[GIH][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12637679	0.82[JPT][hapmap]
rs13059817	0.82[JPT][hapmap]
rs13062423	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13084780	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs13098554	0.82[JPT][hapmap]
rs13098789	0.92[ASN][1000 genomes]
rs1563615	0.80[CHB][hapmap];0.82[JPT][hapmap]
rs1625751	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1672927	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1672928	0.85[CHB][hapmap];0.82[JPT][hapmap]
rs1672932	0.95[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1672963	0.92[ASN][1000 genomes]
rs1673594	0.90[ASN][1000 genomes]
rs1673608	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1673622	0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs1679165	0.88[ASN][1000 genomes]
rs1679168	0.87[CEU][hapmap];0.90[TSI][hapmap]
rs1679169	0.88[ASN][1000 genomes]
rs1720833	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2086351	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2280596	0.80[ASN][1000 genomes]
rs2347469	0.92[TSI][hapmap]
rs2607790	0.92[ASN][1000 genomes]
rs28719641	0.91[ASN][1000 genomes]
rs34416776	0.80[ASN][1000 genomes]
rs34607531	0.80[ASN][1000 genomes]
rs34878008	0.80[ASN][1000 genomes]
rs35471402	0.96[ASN][1000 genomes]
rs35500947	0.89[ASN][1000 genomes]
rs35932955	0.84[ASN][1000 genomes]
rs3813264	0.91[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3884240	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3884241	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4678265	0.82[EUR][1000 genomes]
rs4678266	0.99[ASN][1000 genomes]
rs4894389	0.92[ASN][1000 genomes]
rs497334	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs503922	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs529615	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs537210	0.87[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs542010	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs56394118	0.88[ASN][1000 genomes]
rs564800	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs582386	0.92[ASN][1000 genomes]
rs60371967	0.80[ASN][1000 genomes]
rs609797	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs612471	0.91[ASN][1000 genomes]
rs620035	0.92[ASN][1000 genomes]
rs6439809	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs6439810	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs656107	0.84[ASN][1000 genomes]
rs6762114	0.92[ASN][1000 genomes]
rs6763380	0.85[ASN][1000 genomes]
rs6771237	0.93[ASN][1000 genomes]
rs73229526	0.93[ASN][1000 genomes]
rs7626226	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7645920	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs773443	0.86[ASN][1000 genomes]
rs773450	0.95[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs774008	0.81[TSI][hapmap]
rs774011	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs774012	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs814022	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs9049	0.81[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs936316	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9822037	0.96[ASN][1000 genomes]
rs9823182	0.93[ASN][1000 genomes]
rs9848938	0.89[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9879213	0.82[EUR][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	nsv877537	chr3:137979007-138215114	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
2	nsv530057	chr3:138014877-138734390	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	esv3447663	chr3:138096329-138273034	Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv999041	chr3:138148812-138347988	Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv522517	chr3:138174523-138297982	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
6	nsv1013074	chr3:138213166-138737688	Strong transcription Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
7	nsv1002612	chr3:138213274-138831792	Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
8	nsv536726	chr3:138213274-138831792	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9855306	CLDN18	cis	parietal	SCAN
rs9855306	CEP70	cis	Muscle Skeletal	GTEx
rs9855306	FAIM	cis	parietal	SCAN
rs9855306	CEP70	cis	parietal	SCAN

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:138194000-138260200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr3:138207000-138223800	Weak transcription	Brain Anterior Caudate	brain
3	chr3:138208400-138227400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr3:138209200-138218400	Weak transcription	Gastric	stomach
5	chr3:138209400-138236800	Weak transcription	Aorta	Aorta
6	chr3:138209800-138258600	Weak transcription	Primary T cells from cord blood	blood
7	chr3:138210000-138218400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr3:138210000-138230200	Weak transcription	Fetal Brain Male	brain
9	chr3:138210200-138222000	Weak transcription	Brain Hippocampus Middle	brain
10	chr3:138210400-138215200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:138210400-138218400	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr3:138210400-138236800	Weak transcription	Brain Substantia Nigra	brain
13	chr3:138210400-138242000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr3:138210800-138260600	Weak transcription	Colonic Mucosa	Colon
15	chr3:138211000-138229400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr3:138211000-138231000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr3:138211000-138236600	Weak transcription	Spleen	Spleen
18	chr3:138211200-138227200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr3:138211200-138260600	Weak transcription	Brain Angular Gyrus	brain
20	chr3:138211400-138230400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr3:138211600-138215200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:138211600-138227400	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr3:138211800-138215200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
24	chr3:138211800-138260600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:138212000-138235000	Weak transcription	Brain Germinal Matrix	brain
26	chr3:138212000-138235800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr3:138212200-138218400	Weak transcription	Fetal Muscle Leg	muscle
28	chr3:138212400-138218400	Weak transcription	Pancreas	Pancrea
29	chr3:138212400-138221200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr3:138212400-138236600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr3:138212400-138236600	Weak transcription	Esophagus	oesophagus
32	chr3:138212600-138216600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:138212600-138217200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr3:138212600-138218400	Weak transcription	Fetal Stomach	stomach
35	chr3:138212600-138224400	Weak transcription	Left Ventricle	heart
36	chr3:138212600-138236600	Weak transcription	Lung	lung
37	chr3:138212600-138250200	Weak transcription	Brain Cingulate Gyrus	brain
38	chr3:138212800-138236800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr3:138212800-138249800	Weak transcription	Small Intestine	intestine
40	chr3:138213000-138216600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr3:138213000-138216600	Weak transcription	Thymus	Thymus
42	chr3:138213000-138217800	Weak transcription	Fetal Brain Female	brain
43	chr3:138213000-138224400	Weak transcription	Fetal Muscle Trunk	muscle
44	chr3:138213200-138215400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr3:138213200-138216600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr3:138213200-138216600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr3:138213200-138218000	Weak transcription	Adipose Nuclei	Adipose
48	chr3:138213200-138218000	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr3:138213200-138218000	Weak transcription	Dnd41	blood
50	chr3:138213200-138236600	Weak transcription	Ovary	ovary

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