Variant report

Variant	rs13229445
Chromosome Location	chr7:38760584-38760585
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs1012976	1.00[ASN][1000 genomes]
rs10224856	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10225415	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10254354	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10270427	1.00[ASN][1000 genomes]
rs10951574	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701656	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701657	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701661	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12701671	0.85[EUR][1000 genomes]
rs13224619	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13224857	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13230196	0.90[EUR][1000 genomes]
rs13235997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13238093	0.93[EUR][1000 genomes]
rs17240051	1.00[ASN][1000 genomes]
rs2040878	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2189854	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214667	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2214668	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2215032	1.00[ASN][1000 genomes]
rs2245773	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286089	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286093	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286101	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392599	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2392610	1.00[ASN][1000 genomes]
rs34349310	0.93[EUR][1000 genomes]
rs34358406	0.93[EUR][1000 genomes]
rs34621392	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34886315	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34997080	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35220172	1.00[ASN][1000 genomes]
rs35400125	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35632362	0.93[EUR][1000 genomes]
rs35667896	0.85[EUR][1000 genomes]
rs35816439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35843038	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36004953	0.85[EUR][1000 genomes]
rs36114334	0.89[EUR][1000 genomes]
rs4720300	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723780	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723781	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723784	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723787	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4723804	1.00[ASN][1000 genomes]
rs57865190	0.91[AFR][1000 genomes]
rs60922992	0.83[AFR][1000 genomes]
rs61155937	0.91[AFR][1000 genomes]
rs6949958	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6951429	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6960945	1.00[ASN][1000 genomes]
rs6963090	1.00[ASN][1000 genomes]
rs6967384	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6975410	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976302	1.00[ASN][1000 genomes]
rs6976579	1.00[ASN][1000 genomes]
rs6979423	1.00[ASN][1000 genomes]
rs71548633	0.96[EUR][1000 genomes]
rs73357129	0.83[AFR][1000 genomes]
rs73357142	0.83[AFR][1000 genomes]
rs73369001	0.89[AFR][1000 genomes]
rs73370706	0.83[AFR][1000 genomes]
rs73370712	0.92[AFR][1000 genomes]
rs73370716	0.91[AFR][1000 genomes]
rs73370730	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73370736	0.91[AFR][1000 genomes]
rs73370740	0.91[AFR][1000 genomes]
rs757685	1.00[ASN][1000 genomes]
rs758088	1.00[ASN][1000 genomes]
rs7782140	1.00[ASN][1000 genomes]
rs7782277	1.00[ASN][1000 genomes]
rs7787423	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7802052	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs976352	0.86[EUR][1000 genomes];1.00[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	nsv887965	chr7:38706384-38793243	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	esv3345954	chr7:38759327-38761275	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13229445	VPS41	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:38749000-38803600	Weak transcription	Fetal Brain Male	brain
2	chr7:38754200-38760600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr7:38754600-38760800	Weak transcription	GM12878-XiMat	blood
4	chr7:38755000-38791200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:38755600-38760800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr7:38755800-38771600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr7:38756200-38763800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr7:38756400-38760600	Weak transcription	Primary T cells from cord blood	blood
9	chr7:38756400-38764600	Weak transcription	Fetal Brain Female	brain
10	chr7:38756800-38764800	Weak transcription	Rectal Smooth Muscle	rectum
11	chr7:38757000-38784200	Weak transcription	HMEC	breast
12	chr7:38757200-38764400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr7:38757200-38764600	Weak transcription	Primary hematopoietic stem cells	blood
14	chr7:38757200-38764600	Weak transcription	Ovary	ovary
15	chr7:38757200-38835400	Weak transcription	Psoas Muscle	Psoas
16	chr7:38757400-38760600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr7:38757400-38760600	Weak transcription	Brain Hippocampus Middle	brain
18	chr7:38757400-38764600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr7:38757600-38760600	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr7:38757600-38760600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr7:38757600-38760600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr7:38757600-38760600	Weak transcription	Adipose Nuclei	Adipose
23	chr7:38757600-38760800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr7:38757600-38761000	Weak transcription	Duodenum Mucosa	Duodenum
25	chr7:38757800-38760600	Weak transcription	Brain Anterior Caudate	brain
26	chr7:38757800-38760800	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr7:38758000-38760600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr7:38758200-38760600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr7:38758200-38760800	Weak transcription	Primary B cells from cord blood	blood
30	chr7:38758400-38760600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr7:38758400-38760600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr7:38758400-38760600	Weak transcription	Dnd41	blood
33	chr7:38758600-38760600	Weak transcription	Fetal Intestine Small	intestine
34	chr7:38758600-38760800	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr7:38758600-38764400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr7:38758600-38764800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr7:38758600-38767000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr7:38758600-38767800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr7:38758600-38780600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr7:38758800-38760600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr7:38758800-38760600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr7:38758800-38760600	Weak transcription	Liver	Liver
43	chr7:38758800-38760600	Weak transcription	Left Ventricle	heart
44	chr7:38758800-38760600	Weak transcription	Pancreas	Pancrea
45	chr7:38758800-38760800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr7:38758800-38760800	Weak transcription	Placenta	Placenta
47	chr7:38758800-38760800	Weak transcription	Stomach Smooth Muscle	stomach
48	chr7:38758800-38764400	Weak transcription	Fetal Muscle Leg	muscle
49	chr7:38758800-38764400	Weak transcription	Lung	lung
50	chr7:38758800-38764800	Weak transcription	H9 Cell Line	embryonic stem cell

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