Variant report

Variant	rs2350315
Chromosome Location	chr12:29426005-29426006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs1006410	0.85[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1072724	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10843376	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10843385	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10843399	0.81[ASN][1000 genomes]
rs11050147	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11050149	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11050168	0.80[CHB][hapmap];0.86[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301475	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578931	0.86[JPT][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12581107	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs17715086	0.80[CHB][hapmap];0.86[JPT][hapmap];0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2016832	0.80[EUR][1000 genomes]
rs2288128	0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2288129	0.80[CHB][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782505	0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3782510	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3948497	0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4277150	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4931170	0.84[AFR][1000 genomes]
rs4931171	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4931174	0.82[ASN][1000 genomes]
rs6487807	0.80[EUR][1000 genomes]
rs7298031	0.80[EUR][1000 genomes]
rs7299283	0.80[CHB][hapmap];0.85[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7313552	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315346	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7358667	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7956305	0.80[EUR][1000 genomes]
rs7964831	0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs986072	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532233	chr12:29009388-29496179	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers 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	40 gene(s)	inside rSNPs	diseases
4	esv3372345	chr12:29425485-29430283	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2350315	RP11-996F15.2	cis	Thyroid	GTEx
rs2350315	RP11-996F15.2	cis	lung	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29410000-29426200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr12:29414400-29434000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr12:29417200-29465400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr12:29419200-29430600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:29419600-29428000	Weak transcription	Fetal Brain Female	brain
6	chr12:29419800-29430400	Weak transcription	Brain Angular Gyrus	brain
7	chr12:29420400-29435000	Weak transcription	HUVEC	blood vessel
8	chr12:29420600-29431600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr12:29421000-29432000	Weak transcription	Adipose Nuclei	Adipose
10	chr12:29421200-29426600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr12:29421600-29426200	Weak transcription	Fetal Muscle Leg	muscle
12	chr12:29421800-29426200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr12:29422000-29455600	Weak transcription	Left Ventricle	heart
14	chr12:29422000-29465000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr12:29422200-29430400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:29422200-29434800	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:29422400-29434400	Weak transcription	Fetal Kidney	kidney
18	chr12:29422800-29427000	Strong transcription	Primary neutrophils fromperipheralblood	blood
19	chr12:29423200-29426200	Strong transcription	Rectal Mucosa Donor 31	rectum
20	chr12:29423400-29426200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr12:29423400-29427000	Strong transcription	Primary monocytes fromperipheralblood	blood
22	chr12:29423400-29427600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:29423600-29427000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr12:29423800-29426200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr12:29424000-29426800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr12:29424400-29427000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr12:29424600-29435200	Weak transcription	Colon Smooth Muscle	Colon
28	chr12:29424800-29426600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr12:29424800-29433400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr12:29424800-29434800	Weak transcription	Dnd41	blood
31	chr12:29425000-29426200	Enhancers	Placenta	Placenta
32	chr12:29425000-29426800	Enhancers	Placenta Amnion	Placenta Amnion
33	chr12:29425000-29427400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:29425000-29434400	Weak transcription	Fetal Stomach	stomach
35	chr12:29425200-29427800	Weak transcription	Stomach Smooth Muscle	stomach
36	chr12:29425200-29435600	Weak transcription	Brain Hippocampus Middle	brain
37	chr12:29425400-29427800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr12:29425600-29428400	Weak transcription	Primary T cells from cord blood	blood
39	chr12:29425800-29426600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr12:29425800-29426800	Enhancers	H1 Cell Line	embryonic stem cell
41	chr12:29425800-29426800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr12:29425800-29426800	Enhancers	HUES6 Cell Line	embryonic stem cell
43	chr12:29425800-29426800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr12:29425800-29426800	Strong transcription	Duodenum Mucosa	Duodenum
45	chr12:29425800-29426800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr12:29425800-29426800	Strong transcription	Spleen	Spleen
47	chr12:29425800-29427000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr12:29426000-29426400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
49	chr12:29426000-29426600	Enhancers	HUES48 Cell Line	embryonic stem cell
50	chr12:29426000-29426600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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