Variant report

Variant	rs11726717
Chromosome Location	chr4:79235313-79235314
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11721837	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11721839	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11722992	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11724700	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11727404	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11732889	0.82[EUR][1000 genomes]
rs1351845	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1351846	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17422620	0.82[EUR][1000 genomes]
rs17456396	0.82[EUR][1000 genomes]
rs17457087	1.00[GIH][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2061063	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs345523	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs345535	0.95[EUR][1000 genomes]
rs55728531	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs58087494	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58917172	0.81[EUR][1000 genomes]
rs59210732	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59389694	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs59810825	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6533573	0.81[EUR][1000 genomes]
rs6820805	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6823481	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6838168	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72657038	0.81[EUR][1000 genomes]
rs72657042	0.82[EUR][1000 genomes]
rs72657044	0.82[EUR][1000 genomes]
rs72657046	0.82[EUR][1000 genomes]
rs72657053	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72657054	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs72657056	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7656172	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7664093	0.81[EUR][1000 genomes]
rs7671142	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7676704	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534024	chr4:78785189-79437403	ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription 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	18 gene(s)	inside rSNPs	diseases
2	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv525530	chr4:79024524-79266563	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
4	nsv1010782	chr4:79057839-79387207	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv829978	chr4:79144453-79291868	Strong transcription Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11726717	HNRNPD	cis	cerebellum	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79198600-79241400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr4:79208800-79236800	Weak transcription	Fetal Intestine Large	intestine
3	chr4:79215800-79237600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr4:79215800-79243800	Weak transcription	Right Ventricle	heart
5	chr4:79220400-79246600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr4:79220400-79246600	Weak transcription	HMEC	breast
7	chr4:79220600-79241400	Weak transcription	Aorta	Aorta
8	chr4:79220800-79243000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr4:79221000-79237400	Weak transcription	Fetal Heart	heart
10	chr4:79221000-79240000	Weak transcription	Psoas Muscle	Psoas
11	chr4:79221200-79263000	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr4:79227000-79241400	Weak transcription	Left Ventricle	heart
13	chr4:79229400-79241000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr4:79229400-79241200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:79229800-79236400	Weak transcription	Fetal Intestine Small	intestine
16	chr4:79229800-79237600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr4:79229800-79257600	Weak transcription	Fetal Stomach	stomach
18	chr4:79230000-79239600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:79230200-79268600	Weak transcription	Pancreas	Pancrea
20	chr4:79230400-79236800	Weak transcription	Fetal Lung	lung
21	chr4:79230400-79237000	Weak transcription	Fetal Kidney	kidney
22	chr4:79230600-79258000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr4:79231000-79235400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr4:79231000-79235800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:79231600-79237400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:79231600-79244400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr4:79231600-79260400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr4:79232000-79236600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr4:79233000-79236800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr4:79233000-79241000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr4:79233200-79235400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr4:79233200-79235400	Weak transcription	HepG2	liver
33	chr4:79233200-79240800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:79233600-79236000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr4:79234400-79235800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr4:79234600-79236600	Weak transcription	HUES64 Cell Line	embryonic stem cell
37	chr4:79234600-79239600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr4:79234600-79242600	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr4:79234800-79236600	Weak transcription	H1 Cell Line	embryonic stem cell
40	chr4:79235000-79239600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:79235000-79241000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr4:79235200-79239000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr4:79235200-79241400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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