Variant report

Variant	rs12386356
Chromosome Location	chr3:121460412-121460413
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1136995	1.00[ASN][1000 genomes]
rs16845505	0.85[CEU][hapmap]
rs59987610	0.91[EUR][1000 genomes]
rs72626328	0.82[EUR][1000 genomes]
rs7638024	1.00[ASN][1000 genomes]
rs9818226	1.00[ASN][1000 genomes]
rs9837315	0.95[EUR][1000 genomes]
rs9841861	0.83[CEU][hapmap];0.89[EUR][1000 genomes]
rs9849087	0.83[CEU][hapmap];0.98[EUR][1000 genomes]
rs9859702	0.91[EUR][1000 genomes]
rs9861782	0.93[EUR][1000 genomes]
rs9863007	0.93[EUR][1000 genomes]
rs9863608	1.00[ASN][1000 genomes]
rs9868875	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs9869689	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs9882312	0.85[CEU][hapmap]
rs9884018	0.83[CEU][hapmap]
rs9968051	0.85[CEU][hapmap];0.88[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	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	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
5	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
6	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
7	nsv829703	chr3:121383290-121534493	Flanking Active TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv516233	chr3:121419301-121670405	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12386356	SLC15A2	Cis_1M	lymphoblastoid	RTeQTL
rs12386356	GOLGB1	cis	multi-tissue	Pritchard
rs12386356	EAF2	Cis_1M	lymphoblastoid	RTeQTL
rs12386356	IQCB1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:121436600-121466600	Weak transcription	Stomach Mucosa	stomach
2	chr3:121439400-121467200	Weak transcription	Small Intestine	intestine
3	chr3:121443400-121464800	Weak transcription	Fetal Brain Male	brain
4	chr3:121444600-121466400	Weak transcription	Rectal Smooth Muscle	rectum
5	chr3:121444800-121466400	Weak transcription	Colonic Mucosa	Colon
6	chr3:121444800-121467200	Weak transcription	Aorta	Aorta
7	chr3:121444800-121467400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:121444800-121467400	Weak transcription	Spleen	Spleen
9	chr3:121445200-121466200	Weak transcription	Fetal Intestine Small	intestine
10	chr3:121445200-121466800	Weak transcription	Thymus	Thymus
11	chr3:121445200-121467400	Weak transcription	Esophagus	oesophagus
12	chr3:121445800-121467000	Weak transcription	Fetal Stomach	stomach
13	chr3:121445800-121467400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr3:121447600-121467000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr3:121447800-121466400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:121447800-121467000	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:121448000-121466400	Weak transcription	Colon Smooth Muscle	Colon
18	chr3:121448000-121466400	Weak transcription	Fetal Kidney	kidney
19	chr3:121448200-121466600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr3:121448400-121466400	Weak transcription	HSMM	muscle
21	chr3:121448400-121466800	Weak transcription	Hela-S3	cervix
22	chr3:121448600-121466400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:121448800-121463600	Weak transcription	Ovary	ovary
24	chr3:121448800-121464600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:121448800-121465600	Weak transcription	HUVEC	blood vessel
26	chr3:121448800-121466400	Weak transcription	Fetal Lung	lung
27	chr3:121448800-121466400	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr3:121448800-121466800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr3:121448800-121467400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr3:121448800-121467400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:121449000-121464800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:121449000-121466400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:121449000-121466400	Weak transcription	HepG2	liver
34	chr3:121449000-121466800	Weak transcription	Primary neutrophils fromperipheralblood	blood
35	chr3:121449000-121467200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr3:121449000-121467200	Weak transcription	Fetal Thymus	thymus
37	chr3:121449600-121464800	Weak transcription	Liver	Liver
38	chr3:121449600-121466400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr3:121449600-121466800	Weak transcription	Primary B cells from cord blood	blood
40	chr3:121449800-121460600	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:121449800-121467000	Weak transcription	Primary T cells fromperipheralblood	blood
42	chr3:121449800-121467200	Weak transcription	Placenta	Placenta
43	chr3:121450000-121466400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr3:121450000-121466400	Weak transcription	Fetal Intestine Large	intestine
45	chr3:121450000-121467000	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:121450400-121463600	Weak transcription	Right Atrium	heart
47	chr3:121450400-121463800	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr3:121450400-121466400	Weak transcription	HSMMtube	muscle
49	chr3:121450400-121466800	Weak transcription	Primary T cells from cord blood	blood
50	chr3:121450400-121467400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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