Variant report

Variant	rs10403738
Chromosome Location	chr19:36724856-36724857
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	chr19:36705688..36707627-chr19:36722412..36724988,2	K562	blood:

Variant related genes	Relation type
ENSG00000196357	Chromatin interaction
ENSG00000167635	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10407835	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10407850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10409983	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10412832	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10415410	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416509	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416742	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10416925	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10419269	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10425166	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11882933	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12459704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12460466	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12461077	1.00[CEU][hapmap];0.92[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12461112	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12461855	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12462725	0.91[CHB][hapmap]
rs2271842	0.91[CHB][hapmap]
rs28414272	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28528757	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2857	0.91[CHB][hapmap]
rs2945955	0.92[CHB][hapmap]
rs3098393	0.92[CHB][hapmap]
rs4361039	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4806284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4806293	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4806294	0.91[JPT][hapmap];0.80[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4806295	0.83[CHB][hapmap];0.84[JPT][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56206115	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56316708	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56686317	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57385903	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57734651	0.87[EUR][1000 genomes]
rs59026641	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59295196	0.86[ASN][1000 genomes]
rs61413061	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62113093	0.83[EUR][1000 genomes]
rs62113146	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7251745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73038028	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73040107	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8106135	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8111860	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3526489	chr19:36306483-36741945	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	esv3526490	chr19:36306483-36741945	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv520020	chr19:36721368-36822594	Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10403738	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs10403738	ZNF545	Cis_1M	lymphoblastoid	RTeQTL
rs10403738	LINC00665	cis	Muscle Skeletal	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36707000-36726800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:36707400-36730200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:36707600-36731800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr19:36708200-36730800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr19:36710000-36725000	ZNF genes & repeats	GM12878-XiMat	blood
6	chr19:36710000-36732200	ZNF genes & repeats	A549	lung
7	chr19:36710000-36732200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:36711200-36728400	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
9	chr19:36711800-36725000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr19:36711800-36726600	Strong transcription	Fetal Muscle Leg	muscle
11	chr19:36713000-36730200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
12	chr19:36713400-36726600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr19:36714000-36731000	Strong transcription	Dnd41	blood
14	chr19:36714400-36731400	ZNF genes & repeats	Liver	Liver
15	chr19:36715200-36731200	Strong transcription	Fetal Brain Female	brain
16	chr19:36715200-36731600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
17	chr19:36715800-36726800	ZNF genes & repeats	Fetal Intestine Small	intestine
18	chr19:36716200-36728600	ZNF genes & repeats	Fetal Intestine Large	intestine
19	chr19:36716400-36726600	Weak transcription	Fetal Heart	heart
20	chr19:36716400-36730000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr19:36716400-36730200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr19:36716600-36725600	Strong transcription	Primary B cells from peripheral blood	blood
23	chr19:36716600-36727200	Strong transcription	Adipose Nuclei	Adipose
24	chr19:36716600-36728200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr19:36716600-36728200	ZNF genes & repeats	Lung	lung
26	chr19:36716600-36731400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
27	chr19:36716800-36725400	Strong transcription	Pancreas	Pancrea
28	chr19:36716800-36728000	Strong transcription	Placenta Amnion	Placenta Amnion
29	chr19:36716800-36730000	Strong transcription	Brain Germinal Matrix	brain
30	chr19:36716800-36730000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
31	chr19:36717000-36725400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr19:36717000-36726400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:36717000-36726600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr19:36717000-36728600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr19:36717000-36728800	Strong transcription	Skeletal Muscle Male	skeletal muscle
36	chr19:36717000-36730200	Strong transcription	Skeletal Muscle Female	skeletal muscle
37	chr19:36717200-36725200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr19:36717200-36725600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr19:36717200-36725600	Strong transcription	Muscle Satellite Cultured Cells	--
40	chr19:36717200-36726400	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr19:36717200-36726600	Strong transcription	HUVEC	blood vessel
42	chr19:36717200-36726600	Strong transcription	Osteobl	bone
43	chr19:36717200-36727200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr19:36717200-36727400	Strong transcription	Rectal Smooth Muscle	rectum
45	chr19:36717600-36726800	Strong transcription	Colon Smooth Muscle	Colon
46	chr19:36717600-36726800	ZNF genes & repeats	Fetal Stomach	stomach
47	chr19:36718400-36727200	Strong transcription	Ovary	ovary
48	chr19:36718400-36727400	Strong transcription	HSMMtube	muscle
49	chr19:36718400-36729000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
50	chr19:36718400-36729000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood

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