Variant report

Variant	rs11749723
Chromosome Location	chr5:68609885-68609886
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:68606839..68610803-chr5:68625940..68628885,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000183323	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10940215	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11741775	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11741826	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11742878	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11745537	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11745591	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11750525	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957698	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12189282	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13154469	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13168973	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13178839	0.82[ASN][1000 genomes]
rs1976101	0.90[CHB][hapmap]
rs28499200	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34449757	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34862981	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs350092	0.90[CHB][hapmap]
rs35316810	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35438259	0.80[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4288083	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62371692	0.85[ASN][1000 genomes]
rs62373182	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs66514959	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs668139	0.88[CHB][hapmap]
rs68083627	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6865481	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6869305	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6877725	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6881767	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6893648	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72767881	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][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	nsv1018151	chr5:68377118-68667581	Enhancers Active TSS Flanking Active TSS Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv1035004	chr5:68405526-68670101	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
3	nsv968921	chr5:68608721-68610701	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11749723	CCDC125	cis	Thyroid	GTEx
rs11749723	MRPS36	Cis_1M	lymphoblastoid	RTeQTL
rs11749723	CCDC125	cis	Skin Sun Exposed Lower leg	GTEx
rs11749723	MRPS36	cis	lymphoblastoid	seeQTL
rs11749723	CCDC125	cis	lung	GTEx
rs11749723	CCDC125	cis	brain	BrainEAC

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:68541200-68620400	Weak transcription	Stomach Mucosa	stomach
2	chr5:68564200-68611200	Weak transcription	Fetal Brain Male	brain
3	chr5:68565600-68627400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:68566800-68610800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr5:68576400-68614400	Weak transcription	Colon Smooth Muscle	Colon
6	chr5:68576400-68627600	Weak transcription	Brain Substantia Nigra	brain
7	chr5:68576400-68627800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr5:68576600-68627800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:68577400-68628200	Weak transcription	Small Intestine	intestine
10	chr5:68577600-68619800	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:68577600-68627400	Weak transcription	NHEK	skin
12	chr5:68577800-68626600	Weak transcription	A549	lung
13	chr5:68581600-68627600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr5:68581800-68611000	Weak transcription	Psoas Muscle	Psoas
15	chr5:68581800-68617800	Weak transcription	Brain Hippocampus Middle	brain
16	chr5:68581800-68626800	Weak transcription	Fetal Brain Female	brain
17	chr5:68581800-68627600	Weak transcription	Brain Anterior Caudate	brain
18	chr5:68582800-68622400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr5:68588600-68615800	Weak transcription	Colonic Mucosa	Colon
20	chr5:68591600-68614000	Weak transcription	Osteobl	bone
21	chr5:68591600-68627600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr5:68596000-68626800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr5:68596600-68612800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr5:68597000-68611400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:68598600-68611000	Strong transcription	Liver	Liver
26	chr5:68599400-68612000	Weak transcription	HepG2	liver
27	chr5:68599600-68627800	Weak transcription	NH-A	brain
28	chr5:68600600-68610000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr5:68600800-68610000	Strong transcription	Primary T cells from cord blood	blood
30	chr5:68601400-68627600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr5:68602400-68611400	Weak transcription	Fetal Muscle Leg	muscle
32	chr5:68605200-68610000	Strong transcription	Duodenum Mucosa	Duodenum
33	chr5:68605200-68610000	Strong transcription	Sigmoid Colon	Sigmoid Colon
34	chr5:68605200-68610600	Weak transcription	HMEC	breast
35	chr5:68605600-68612000	Weak transcription	Ovary	ovary
36	chr5:68605600-68613800	Weak transcription	Brain Germinal Matrix	brain
37	chr5:68605600-68627400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr5:68605800-68611400	Weak transcription	Pancreas	Pancrea
39	chr5:68606200-68610600	Strong transcription	Primary T helper cells fromperipheralblood	blood
40	chr5:68606200-68625600	Weak transcription	Hela-S3	cervix
41	chr5:68606400-68611200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr5:68607400-68612600	Strong transcription	Fetal Intestine Small	intestine
43	chr5:68607800-68610000	Strong transcription	Adipose Nuclei	Adipose
44	chr5:68607800-68610000	Strong transcription	Left Ventricle	heart
45	chr5:68608000-68610000	Strong transcription	Fetal Stomach	stomach
46	chr5:68608000-68610000	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr5:68608000-68610400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr5:68608000-68610600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr5:68608000-68610600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr5:68608200-68610000	Strong transcription	Fetal Intestine Large	intestine

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