Variant report

Variant	rs11673344
Chromosome Location	chr19:37684966-37684967
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs1047333	0.88[CEU][hapmap];0.85[GIH][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes]
rs11084871	0.82[EUR][1000 genomes]
rs11666897	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11667146	0.92[CEU][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes]
rs11670216	0.82[EUR][1000 genomes]
rs11671112	0.80[EUR][1000 genomes]
rs11673192	0.82[EUR][1000 genomes]
rs12151313	0.85[EUR][1000 genomes]
rs1234251	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1533736	0.88[CEU][hapmap]
rs17707446	0.81[CEU][hapmap]
rs1879497	0.92[CEU][hapmap];0.86[GIH][hapmap];0.93[TSI][hapmap];0.88[EUR][1000 genomes]
rs1962889	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2011475	0.82[EUR][1000 genomes]
rs2562587	0.82[EUR][1000 genomes]
rs3745768	0.88[CEU][hapmap]
rs3745770	0.88[CEU][hapmap]
rs45626541	0.98[EUR][1000 genomes]
rs55792845	0.83[EUR][1000 genomes]
rs55921822	0.83[EUR][1000 genomes]
rs56208574	0.83[EUR][1000 genomes]
rs56330606	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56343212	0.80[EUR][1000 genomes]
rs703530	0.82[EUR][1000 genomes]
rs703535	0.81[EUR][1000 genomes]
rs703537	0.82[EUR][1000 genomes]
rs7247589	0.82[EUR][1000 genomes]
rs7254616	0.81[EUR][1000 genomes]
rs7256213	0.82[EUR][1000 genomes]
rs7256746	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7256876	0.86[EUR][1000 genomes]
rs7257135	0.81[CEU][hapmap]
rs7259513	0.86[EUR][1000 genomes]
rs7260386	0.92[CEU][hapmap];0.83[CHB][hapmap];0.82[YRI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs73622783	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8104919	0.82[EUR][1000 genomes]
rs8106386	0.82[EUR][1000 genomes]
rs8107192	0.81[EUR][1000 genomes]
rs8108727	0.92[CEU][hapmap];0.87[EUR][1000 genomes]
rs826322	0.82[EUR][1000 genomes]
rs826323	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
5	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
8	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
9	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
13	nsv911655	chr19:37646745-37758082	ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs11673344	MED29	cis	cerebellum	SCAN
rs11673344	AC012309.5	cis	Heart Left Ventricle	GTEx
rs11673344	ZNF585B	cis	Artery Tibial	GTEx
rs11673344	AC012309.5	cis	Esophagus Muscularis	GTEx
rs11673344	AC012309.5	cis	Artery Tibial	GTEx
rs11673344	AC012309.5	cis	Thyroid	GTEx
rs11673344	PAK4	cis	cerebellum	SCAN
rs11673344	B9D2	cis	parietal	SCAN
rs11673344	C19orf61	cis	cerebellum	SCAN
rs11673344	ZNF585A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37668000-37686000	ZNF genes & repeats	Liver	Liver
2	chr19:37672000-37686400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
3	chr19:37672200-37686000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr19:37672800-37686000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr19:37673200-37690600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
6	chr19:37673400-37685400	ZNF genes & repeats	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr19:37673800-37685600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr19:37675000-37701000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr19:37676600-37685200	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr19:37676800-37686000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
11	chr19:37676800-37686000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
12	chr19:37677000-37685600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
13	chr19:37677000-37686000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr19:37677000-37686000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr19:37677000-37686000	Strong transcription	Placenta Amnion	Placenta Amnion
16	chr19:37677000-37686200	ZNF genes & repeats	Ovary	ovary
17	chr19:37677200-37685400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr19:37677200-37687600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
19	chr19:37677400-37685000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
20	chr19:37678400-37685000	Strong transcription	Brain Anterior Caudate	brain
21	chr19:37678600-37686200	ZNF genes & repeats	Fetal Intestine Large	intestine
22	chr19:37679000-37685400	ZNF genes & repeats	Fetal Stomach	stomach
23	chr19:37679000-37700800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr19:37679800-37686400	Strong transcription	Brain Hippocampus Middle	brain
25	chr19:37680600-37685200	Strong transcription	Skeletal Muscle Male	skeletal muscle
26	chr19:37680600-37700800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr19:37680800-37685400	Strong transcription	Brain Inferior Temporal Lobe	brain
28	chr19:37680800-37685800	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr19:37680800-37689800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:37680800-37695000	Weak transcription	HSMM	muscle
31	chr19:37680800-37700800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr19:37680800-37700800	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr19:37681000-37687400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr19:37681000-37690800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr19:37681000-37695800	Weak transcription	NH-A	brain
36	chr19:37681000-37695800	Weak transcription	NHLF	lung
37	chr19:37681000-37700800	Weak transcription	HSMMtube	muscle
38	chr19:37681000-37700800	Weak transcription	HUVEC	blood vessel
39	chr19:37681000-37701000	Weak transcription	Fetal Heart	heart
40	chr19:37681200-37696600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr19:37681600-37690600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr19:37682000-37685200	ZNF genes & repeats	Colon Smooth Muscle	Colon
43	chr19:37682000-37686000	ZNF genes & repeats	Adipose Nuclei	Adipose
44	chr19:37682200-37685200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
45	chr19:37682400-37685800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
46	chr19:37682400-37685800	Strong transcription	Brain Germinal Matrix	brain
47	chr19:37682400-37688600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr19:37682600-37685000	Strong transcription	Stomach Smooth Muscle	stomach
49	chr19:37682600-37685600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
50	chr19:37682800-37689200	Weak transcription	Right Ventricle	heart

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