Variant report

Variant	rs3809116
Chromosome Location	chr12:122715535-122715536
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:122715428..122718319-chr12:122718788..122721309,2	MCF-7	breast:
2	chr12:122711907..122714126-chr12:122714417..122716211,2	K562	blood:

Variant related genes	Relation type
ENSG00000184047	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10270	0.83[CEU][hapmap];0.80[CHB][hapmap];0.85[JPT][hapmap]
rs10848035	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11060167	0.95[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs11060333	0.95[CEU][hapmap];0.89[TSI][hapmap];0.86[EUR][1000 genomes]
rs12423987	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs12424872	0.83[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12425684	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12578739	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12578815	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12578863	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12580084	0.83[CEU][hapmap];0.85[JPT][hapmap]
rs12809220	0.87[EUR][1000 genomes]
rs12810587	0.91[CEU][hapmap]
rs12811503	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12814516	0.89[EUR][1000 genomes]
rs12814554	0.81[EUR][1000 genomes]
rs12814923	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs12816400	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12816499	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12820704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12822121	0.91[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12824385	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12824701	0.91[CEU][hapmap];0.81[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap];0.81[MEX][hapmap]
rs12824925	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12825008	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12825149	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs12825279	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12826834	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12827843	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12831210	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1512023	0.91[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.80[EUR][1000 genomes]
rs1967291	0.88[EUR][1000 genomes]
rs2063510	0.81[JPT][hapmap]
rs2068223	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2271408	1.00[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2271409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2277332	0.80[JPT][hapmap]
rs2277333	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34383196	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35030971	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35772530	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35963777	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3782154	0.80[JPT][hapmap]
rs4567503	0.81[JPT][hapmap]
rs4758649	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];0.96[TSI][hapmap];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4758650	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs4758670	0.82[CHD][hapmap];0.85[JPT][hapmap]
rs4758677	0.95[CEU][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs6488906	0.85[EUR][1000 genomes]
rs6488909	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7388	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7962385	0.83[CEU][hapmap];0.80[CHD][hapmap];0.81[JPT][hapmap]
rs7963565	0.83[CEU][hapmap];0.86[JPT][hapmap]
rs7970027	0.83[CEU][hapmap];0.81[JPT][hapmap]
rs872451	0.91[CEU][hapmap]
rs907482	0.83[CEU][hapmap];0.81[JPT][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529868	chr12:121956483-122944265	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	173 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs3809116	VPS33A	cis	lymphoblastoid	seeQTL
rs3809116	VPS33A	cis	brain	seeQTL
rs3809116	GPR109A	cis	cerebellum	SCAN
rs3809116	VPS33A	cis	multi-tissue	Pritchard
rs3809116	IL31	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:122710800-122716600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:122711400-122715600	Weak transcription	Fetal Kidney	kidney
3	chr12:122711400-122734200	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:122711600-122715800	Weak transcription	Fetal Heart	heart
5	chr12:122711600-122718000	Weak transcription	A549	lung
6	chr12:122711600-122720200	Weak transcription	HUVEC	blood vessel
7	chr12:122711600-122721800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:122711800-122715800	Weak transcription	Right Atrium	heart
9	chr12:122711800-122716600	Weak transcription	NHDF-Ad	bronchial
10	chr12:122711800-122718400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr12:122711800-122719000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr12:122711800-122720200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr12:122711800-122720200	Weak transcription	Small Intestine	intestine
14	chr12:122711800-122734400	Weak transcription	Stomach Mucosa	stomach
15	chr12:122711800-122734800	Weak transcription	Fetal Brain Male	brain
16	chr12:122711800-122749600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr12:122711800-122749600	Weak transcription	Psoas Muscle	Psoas
18	chr12:122712000-122715600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr12:122712000-122730000	Strong transcription	Fetal Intestine Large	intestine
20	chr12:122712200-122719200	Weak transcription	NHLF	lung
21	chr12:122712200-122722000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:122712200-122730800	Strong transcription	Fetal Muscle Trunk	muscle
23	chr12:122712400-122720600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr12:122712400-122748600	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr12:122713200-122715600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr12:122713200-122715800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr12:122713200-122715800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr12:122713400-122715600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr12:122713400-122722000	Strong transcription	Left Ventricle	heart
30	chr12:122713600-122716200	Strong transcription	HSMM	muscle
31	chr12:122713600-122720600	Strong transcription	Primary B cells from cord blood	blood
32	chr12:122713600-122722000	Strong transcription	Stomach Smooth Muscle	stomach
33	chr12:122713600-122725000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr12:122713600-122726800	Strong transcription	Primary T cells fromperipheralblood	blood
35	chr12:122713800-122719800	Strong transcription	Liver	Liver
36	chr12:122713800-122722000	Strong transcription	Placenta	Placenta
37	chr12:122713800-122722200	Strong transcription	Duodenum Smooth Muscle	Duodenum
38	chr12:122713800-122726800	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr12:122713800-122727800	Strong transcription	Fetal Thymus	thymus
40	chr12:122713800-122729400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:122713800-122730800	Strong transcription	Adipose Nuclei	Adipose
42	chr12:122713800-122731000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
43	chr12:122713800-122731000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:122713800-122748800	Strong transcription	Primary monocytes fromperipheralblood	blood
45	chr12:122714000-122717800	Strong transcription	Primary T helper naive cells from peripheral blood	blood
46	chr12:122714000-122720200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:122714000-122720600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr12:122714000-122722000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr12:122714000-122723800	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr12:122714000-122727000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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