Variant report

Variant	rs9868286
Chromosome Location	chr3:191081486-191081487
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:191080948..191083585-chr3:191091535..191093381,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs13326246	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13434281	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17545865	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17754685	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs17811727	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2164237	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs28368295	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28448537	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28502671	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs28510847	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4677634	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4687210	0.94[CEU][hapmap];0.93[MEX][hapmap];0.90[TSI][hapmap];0.87[EUR][1000 genomes]
rs9290985	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs980320	0.95[EUR][1000 genomes]
rs980321	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9825936	0.94[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9826141	0.95[EUR][1000 genomes]
rs9827142	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9839989	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9844109	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9855282	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9868495	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 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	nsv508266	chr3:191064212-191083637	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	esv1808657	chr3:191064330-191081793	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
10	esv1823184	chr3:191064803-191082303	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	esv1848120	chr3:191064803-191082303	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	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
13	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
14	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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs9868286	CCDC50	cis	Artery Tibial	GTEx
rs9868286	CCDC50	cis	Esophagus Muscularis	GTEx
rs9868286	CCDC50	cis	Thyroid	GTEx
rs9868286	FBXO45	cis	parietal	SCAN
rs9868286	CCDC50	cis	Nerve Tibial	GTEx

Chromatin state (count:113 , 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	chr3:191071000-191088400	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr3:191071200-191114000	Weak transcription	Colonic Mucosa	Colon
4	chr3:191071400-191094200	Weak transcription	Small Intestine	intestine
5	chr3:191071400-191097400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr3:191071400-191100000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:191072600-191100800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr3:191073600-191083000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:191073600-191090000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr3:191074600-191092800	Weak transcription	Esophagus	oesophagus
11	chr3:191074600-191094000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr3:191074800-191081800	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr3:191074800-191083000	Strong transcription	Primary B cells from cord blood	blood
14	chr3:191074800-191085800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:191074800-191094200	Weak transcription	A549	lung
16	chr3:191075000-191082200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr3:191075000-191097400	Weak transcription	Thymus	Thymus
18	chr3:191075200-191081600	Strong transcription	Duodenum Mucosa	Duodenum
19	chr3:191075200-191081600	Strong transcription	NHLF	lung
20	chr3:191075200-191084200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
21	chr3:191075400-191081800	Strong transcription	HSMM	muscle
22	chr3:191075400-191082000	Strong transcription	Liver	Liver
23	chr3:191075400-191082800	Strong transcription	Fetal Brain Female	brain
24	chr3:191075600-191081600	Strong transcription	K562	blood
25	chr3:191075600-191081800	Strong transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:191075600-191082000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr3:191075600-191082000	Strong transcription	Stomach Smooth Muscle	stomach
28	chr3:191075600-191082200	Strong transcription	Osteobl	bone
29	chr3:191075600-191083000	Strong transcription	Fetal Intestine Large	intestine
30	chr3:191075600-191084200	Strong transcription	Muscle Satellite Cultured Cells	--
31	chr3:191075600-191084600	Strong transcription	Fetal Lung	lung
32	chr3:191075600-191087000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr3:191075800-191081800	Strong transcription	Placenta	Placenta
34	chr3:191075800-191081800	Strong transcription	HSMMtube	muscle
35	chr3:191075800-191082000	Strong transcription	Adipose Nuclei	Adipose
36	chr3:191075800-191082000	Strong transcription	Fetal Muscle Leg	muscle
37	chr3:191075800-191082200	Strong transcription	Fetal Muscle Trunk	muscle
38	chr3:191075800-191083000	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr3:191075800-191085200	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr3:191076000-191082800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:191076000-191088800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
42	chr3:191076000-191092800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr3:191076200-191091000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:191076800-191082200	Strong transcription	Left Ventricle	heart
45	chr3:191077200-191081600	Strong transcription	Hela-S3	cervix
46	chr3:191077200-191082000	Strong transcription	NH-A	brain
47	chr3:191077200-191086600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
48	chr3:191077400-191082200	Strong transcription	Rectal Smooth Muscle	rectum
49	chr3:191077600-191084600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:191077600-191094200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links