Variant report

Variant	rs10989528
Chromosome Location	chr9:104244512-104244513
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	chr9:104242678..104246485-chr9:104246674..104250284,6	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RNF20-1	chr9:104243645-104244538	NONHSAT133735

Variant related genes	Relation type
ENSG00000165152	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10819945	0.89[ASN][1000 genomes]
rs10989529	0.93[ASN][1000 genomes]
rs16920420	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4742815	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57815349	0.80[EUR][1000 genomes];0.89[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	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv893626	chr9:104172936-104324545	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10989528	TMEM246	cis	Nerve Tibial	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104227800-104248200	Weak transcription	Liver	Liver
2	chr9:104229000-104248200	Weak transcription	NHLF	lung
3	chr9:104230800-104248200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:104231000-104248000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr9:104234400-104248200	Weak transcription	Fetal Kidney	kidney
6	chr9:104238800-104246400	Weak transcription	Fetal Brain Male	brain
7	chr9:104239000-104247800	Weak transcription	A549	lung
8	chr9:104239200-104244600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr9:104239200-104247800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr9:104239200-104247800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr9:104239200-104247800	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr9:104239200-104247800	Weak transcription	Fetal Lung	lung
13	chr9:104239200-104247800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr9:104239200-104248000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:104239200-104248000	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:104239200-104248200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr9:104239200-104248200	Weak transcription	Fetal Muscle Trunk	muscle
18	chr9:104239400-104245000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr9:104239400-104247800	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr9:104239400-104247800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr9:104239400-104247800	Weak transcription	Fetal Stomach	stomach
22	chr9:104239400-104248000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr9:104239400-104248000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:104239400-104248000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr9:104239400-104248000	Weak transcription	Brain Germinal Matrix	brain
26	chr9:104239800-104244600	Enhancers	Stomach Mucosa	stomach
27	chr9:104240600-104244800	Enhancers	Pancreas	Pancrea
28	chr9:104240800-104244600	Enhancers	Fetal Intestine Small	intestine
29	chr9:104241000-104246800	Weak transcription	Fetal Muscle Leg	muscle
30	chr9:104241000-104247800	Enhancers	Fetal Heart	heart
31	chr9:104241000-104248200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr9:104241200-104246400	Weak transcription	Colon Smooth Muscle	Colon
33	chr9:104241200-104247800	Weak transcription	Fetal Brain Female	brain
34	chr9:104241600-104245000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr9:104241800-104248200	Weak transcription	Aorta	Aorta
36	chr9:104242200-104247800	Weak transcription	Brain Cingulate Gyrus	brain
37	chr9:104242200-104248200	Weak transcription	Gastric	stomach
38	chr9:104242200-104248200	Weak transcription	Psoas Muscle	Psoas
39	chr9:104242400-104245000	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:104242600-104245400	Enhancers	Brain Angular Gyrus	brain
41	chr9:104242800-104244800	Enhancers	Duodenum Mucosa	Duodenum
42	chr9:104242800-104246600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr9:104242800-104247800	Weak transcription	Brain Anterior Caudate	brain
44	chr9:104243000-104247800	Weak transcription	Adipose Nuclei	Adipose
45	chr9:104243000-104248200	Weak transcription	Brain Substantia Nigra	brain
46	chr9:104243200-104245800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr9:104243600-104245800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
48	chr9:104243800-104244800	Enhancers	Left Ventricle	heart
49	chr9:104243800-104247800	Weak transcription	Right Atrium	heart
50	chr9:104243800-104248000	Weak transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links