Variant report

Variant	rs497789
Chromosome Location	chr9:14102939-14102940
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10756530	0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10756531	0.85[CEU][hapmap]
rs10810093	0.86[CHB][hapmap];0.84[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1689280	0.81[EUR][1000 genomes]
rs35870361	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs480700	0.80[AMR][1000 genomes]
rs484555	0.86[CHB][hapmap];0.86[GIH][hapmap];0.87[MEX][hapmap]
rs508940	0.95[CEU][hapmap];0.82[CHB][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs510777	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs516075	0.86[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs516090	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs516325	0.80[EUR][1000 genomes]
rs574460	0.82[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs580501	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs580845	0.81[CHD][hapmap];0.86[GIH][hapmap];0.83[AMR][1000 genomes]
rs7019649	0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[GIH][hapmap];0.86[JPT][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7034211	0.81[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs7862890	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active 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 miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats 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	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs497789	C9orf93	cis	cerebellum	SCAN
rs497789	CCDC92	trans	parietal	SCAN

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14075400-14116000	Weak transcription	Gastric	stomach
2	chr9:14078000-14112800	Weak transcription	Duodenum Mucosa	Duodenum
3	chr9:14081400-14115800	Weak transcription	Hela-S3	cervix
4	chr9:14086000-14115600	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr9:14090600-14115200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr9:14096800-14120000	Weak transcription	Brain Substantia Nigra	brain
7	chr9:14097400-14103200	Weak transcription	Brain Angular Gyrus	brain
8	chr9:14097400-14111800	Weak transcription	Left Ventricle	heart
9	chr9:14097400-14135400	Weak transcription	HSMMtube	muscle
10	chr9:14097600-14112400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr9:14097800-14107600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr9:14097800-14111800	Weak transcription	HMEC	breast
13	chr9:14098200-14106600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr9:14098400-14103000	Weak transcription	NHEK	skin
15	chr9:14098400-14115800	Weak transcription	Rectal Mucosa Donor 29	rectum
16	chr9:14098800-14103000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr9:14098800-14107600	Weak transcription	Fetal Intestine Small	intestine
18	chr9:14098800-14115600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
19	chr9:14098800-14116000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr9:14099000-14107600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:14099000-14111800	Weak transcription	Pancreas	Pancrea
22	chr9:14099000-14112200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:14099000-14112600	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:14099000-14113600	Weak transcription	Fetal Brain Male	brain
25	chr9:14099000-14115600	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr9:14099000-14116000	Weak transcription	Psoas Muscle	Psoas
27	chr9:14099200-14103000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr9:14099200-14106400	Weak transcription	Fetal Stomach	stomach
29	chr9:14099200-14106600	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr9:14099200-14111600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr9:14099200-14111800	Weak transcription	NH-A	brain
32	chr9:14099200-14112600	Weak transcription	Osteobl	bone
33	chr9:14100000-14103600	Weak transcription	Colon Smooth Muscle	Colon
34	chr9:14100000-14106600	Weak transcription	Cortex derived primary cultured neurospheres	brain
35	chr9:14100000-14108000	Weak transcription	Right Ventricle	heart
36	chr9:14100000-14112200	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr9:14100200-14111200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr9:14100200-14112600	Weak transcription	Fetal Muscle Leg	muscle
39	chr9:14101000-14113000	Weak transcription	Placenta	Placenta
40	chr9:14101800-14103400	Enhancers	ES-I3 Cell Line	embryonic stem cell
41	chr9:14101800-14103400	Strong transcription	HUVEC	blood vessel
42	chr9:14101800-14108600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr9:14101800-14128200	Weak transcription	Esophagus	oesophagus
44	chr9:14102000-14103400	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr9:14102200-14103000	Strong transcription	Liver	Liver
46	chr9:14102200-14103200	Enhancers	HUES48 Cell Line	embryonic stem cell
47	chr9:14102200-14103200	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr9:14102200-14103200	Enhancers	HSMM	muscle
49	chr9:14102400-14103000	Genic enhancers	Brain Germinal Matrix	brain
50	chr9:14102400-14103000	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links