Variant report

Variant	rs9839989
Chromosome Location	chr3:191088566-191088567
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13326246	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13434281	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17545865	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17754685	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17811727	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2164237	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs28368295	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28448537	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28502671	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs28510847	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4677634	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4687210	0.88[EUR][1000 genomes]
rs9290985	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs980320	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs980321	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9812544	0.80[AFR][1000 genomes]
rs9825936	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9826141	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9827142	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9844109	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9855282	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9868286	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9868495	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428100	chr3:190793797-191092633	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv931943	chr3:190860224-191321873	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv2757910	chr3:190867011-191279107	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv2759209	chr3:190867011-191279107	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv428428	chr3:190936834-191215596	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv998208	chr3:191021434-191175350	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv534269	chr3:191037181-191261730	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv878107	chr3:191069984-191100073	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv592852	chr3:191073228-191093310	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
10	nsv592853	chr3:191073228-191094985	Strong transcription Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs9839989	CCDC50	cis	Artery Tibial	GTEx
rs9839989	CCDC50	cis	Thyroid	GTEx
rs9839989	CCDC50	cis	Nerve Tibial	GTEx
rs9839989	CCDC50	cis	Esophagus Muscularis	GTEx

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:191069800-191096000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
3	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
4	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr3:191073600-191090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr3:191074600-191092800	Weak transcription	Esophagus	oesophagus
9	chr3:191074600-191094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr3:191074800-191094200	Weak transcription	A549	lung
11	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
12	chr3:191076000-191088800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr3:191076000-191092800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr3:191076200-191091000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:191077600-191094200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:191078000-191089200	Strong transcription	Primary B cells from peripheral blood	blood
17	chr3:191079400-191093000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr3:191079400-191094200	Weak transcription	Brain Anterior Caudate	brain
19	chr3:191079400-191094800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr3:191079400-191115800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr3:191079600-191088800	Weak transcription	Fetal Brain Male	brain
22	chr3:191079600-191089800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:191079600-191089800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr3:191079600-191092600	Weak transcription	Primary T cells from cord blood	blood
25	chr3:191079600-191099200	Weak transcription	Spleen	Spleen
26	chr3:191079600-191116400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:191079600-191121200	Weak transcription	Gastric	stomach
28	chr3:191079800-191094200	Weak transcription	Brain Substantia Nigra	brain
29	chr3:191080200-191094600	Weak transcription	Stomach Mucosa	stomach
30	chr3:191080200-191110200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:191080200-191118800	Weak transcription	Pancreas	Pancrea
32	chr3:191080400-191092800	Weak transcription	Fetal Intestine Small	intestine
33	chr3:191080600-191088800	Weak transcription	Lung	lung
34	chr3:191080600-191092800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr3:191080600-191094200	Weak transcription	Right Ventricle	heart
36	chr3:191080600-191094400	Weak transcription	Brain Angular Gyrus	brain
37	chr3:191080600-191110400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:191081600-191094200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr3:191081800-191088600	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr3:191081800-191090200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
41	chr3:191081800-191092800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr3:191082000-191088800	Weak transcription	GM12878-XiMat	blood
43	chr3:191082200-191092800	Weak transcription	Aorta	Aorta
44	chr3:191082400-191092800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr3:191082800-191090400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:191083000-191094800	Strong transcription	Liver	Liver
47	chr3:191083400-191092800	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr3:191084000-191089200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr3:191084200-191094200	Weak transcription	Colon Smooth Muscle	Colon
50	chr3:191084400-191090400	Strong transcription	Monocytes-CD14+_RO01746	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links