Variant report

Variant	rs3815843
Chromosome Location	chr12:29501906-29501907
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs10082724	0.84[AFR][1000 genomes]
rs10082956	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10128781	0.88[YRI][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1035606	0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1035607	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10843388	0.85[AFR][1000 genomes]
rs10843390	0.88[YRI][hapmap];0.84[AMR][1000 genomes]
rs10843391	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10843393	0.83[AFR][1000 genomes]
rs10843397	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10843398	0.91[YRI][hapmap]
rs11050175	1.00[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11050203	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050209	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1156242	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12320212	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12831751	0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2278093	0.91[YRI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2278094	0.91[YRI][hapmap]
rs3782513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6487815	0.87[YRI][hapmap]
rs7136223	0.84[AMR][1000 genomes]
rs7297435	0.92[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7311742	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7315504	0.83[YRI][hapmap]
rs7953619	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9651802	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs966540	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs966541	0.90[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs996498	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9989017	0.94[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[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	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
2	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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3815843	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx
rs3815843	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs3815843	ERGIC2	cis	multi-tissue	Pritchard
rs3815843	MLSTD1	cis	normal skin	skin_eQTL
rs3815843	RP11-996F15.2	cis	Stomach	GTEx
rs3815843	RP11-996F15.2	cis	lung	GTEx
rs3815843	RP11-996F15.2	cis	Thyroid	GTEx
rs3815843	RP11-996F15.2	cis	Artery Aorta	GTEx
rs3815843	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs3815843	RP11-996F15.2	cis	Esophagus Muscularis	GTEx
rs3815843	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs3815843	RP11-996F15.2	cis	Artery Tibial	GTEx
rs3815843	RP11-996F15.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
5	chr12:29473800-29522600	Weak transcription	NHEK	skin
6	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
8	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
10	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
16	chr12:29485600-29533400	Weak transcription	Gastric	stomach
17	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
18	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr12:29488600-29503800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr12:29488800-29532000	Weak transcription	NHLF	lung
21	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
23	chr12:29490000-29502800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
26	chr12:29490200-29502000	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr12:29490200-29502200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr12:29490200-29506000	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr12:29490400-29502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:29490600-29502000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr12:29490600-29503000	Strong transcription	Primary monocytes fromperipheralblood	blood
33	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr12:29491200-29502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
36	chr12:29492200-29502800	Strong transcription	Placenta	Placenta
37	chr12:29492400-29502000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:29492400-29511800	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr12:29492400-29518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr12:29492800-29511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:29492800-29519000	Weak transcription	HepG2	liver
42	chr12:29493000-29503200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr12:29493200-29504800	Strong transcription	Primary T helper cells fromperipheralblood	blood
44	chr12:29493600-29532600	Weak transcription	Skeletal Muscle Male	skeletal muscle
45	chr12:29494400-29517800	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr12:29494400-29532400	Weak transcription	Brain Substantia Nigra	brain
47	chr12:29494600-29509000	Weak transcription	Lung	lung
48	chr12:29494600-29511800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:29494600-29532800	Weak transcription	Colonic Mucosa	Colon
50	chr12:29495800-29503400	Strong transcription	HUES6 Cell Line	embryonic stem cell

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