Variant report

Variant	rs10817771
Chromosome Location	chr9:100324560-100324561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100262480..100265797-chr9:100324164..100327795,3	K562	blood:
2	chr9:100316877..100321720-chr9:100323488..100327192,5	K562	blood:
3	chr9:100324071..100326251-chr9:100329455..100331958,2	K562	blood:
4	chr9:100293612..100296079-chr9:100323288..100324987,2	K562	blood:

Variant related genes	Relation type
ENSG00000136842	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10759781	0.83[JPT][hapmap]
rs10817760	0.80[ASN][1000 genomes]
rs10982730	0.85[ASN][1000 genomes]
rs10982736	0.87[ASN][1000 genomes]
rs10982748	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11795334	0.85[ASN][1000 genomes]
rs12004491	0.82[EUR][1000 genomes]
rs12379728	0.85[ASN][1000 genomes]
rs1475543	0.83[ASN][1000 genomes]
rs1475545	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7875496	0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[MEX][hapmap]

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	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10817771	C9orf156	cis	cerebellum	SCAN
rs10817771	HSD17B3	cis	parietal	SCAN
rs10817771	TMOD1	cis	cerebellum	SCAN
rs10817771	SLC35D2	cis	parietal	SCAN

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100311800-100325200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr9:100315600-100326200	Weak transcription	Esophagus	oesophagus
3	chr9:100319200-100327400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr9:100320000-100326200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr9:100320000-100326200	Weak transcription	Pancreas	Pancrea
6	chr9:100320000-100326200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr9:100320000-100326600	Weak transcription	Gastric	stomach
8	chr9:100320400-100324600	Weak transcription	Fetal Muscle Leg	muscle
9	chr9:100320400-100326400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr9:100320600-100326000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr9:100320800-100325600	Weak transcription	Aorta	Aorta
12	chr9:100321200-100325000	Strong transcription	K562	blood
13	chr9:100321400-100325400	Weak transcription	Adipose Nuclei	Adipose
14	chr9:100321600-100324800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr9:100321600-100325400	Weak transcription	Fetal Brain Female	brain
16	chr9:100321600-100326000	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr9:100321600-100326400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr9:100321600-100331400	Weak transcription	Liver	Liver
19	chr9:100321800-100326200	Weak transcription	Colon Smooth Muscle	Colon
20	chr9:100322000-100326000	Weak transcription	Fetal Brain Male	brain
21	chr9:100322400-100324600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr9:100323200-100325000	Enhancers	Lung	lung
23	chr9:100323200-100325400	Enhancers	Right Atrium	heart
24	chr9:100323200-100325800	Enhancers	Brain Hippocampus Middle	brain
25	chr9:100323200-100326000	Enhancers	Brain Substantia Nigra	brain
26	chr9:100323200-100326200	Enhancers	Brain Cingulate Gyrus	brain
27	chr9:100323200-100327200	Enhancers	Left Ventricle	heart
28	chr9:100323200-100327400	Enhancers	Right Ventricle	heart
29	chr9:100323600-100325200	Genic enhancers	Brain Anterior Caudate	brain
30	chr9:100323600-100326400	Weak transcription	HSMMtube	muscle
31	chr9:100323800-100324800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr9:100323800-100325000	Weak transcription	Psoas Muscle	Psoas
33	chr9:100324000-100327600	Genic enhancers	Ovary	ovary
34	chr9:100324200-100324600	Genic enhancers	Brain Angular Gyrus	brain
35	chr9:100324200-100324800	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr9:100324200-100326200	Enhancers	Brain Germinal Matrix	brain
37	chr9:100324200-100327400	Weak transcription	GM12878-XiMat	blood
38	chr9:100324200-100333200	Weak transcription	Spleen	Spleen
39	chr9:100324400-100325800	Genic enhancers	Fetal Heart	heart
40	chr9:100324400-100326600	Genic enhancers	Skeletal Muscle Male	skeletal muscle
41	chr9:100324400-100326800	Genic enhancers	Stomach Smooth Muscle	stomach
42	chr9:100324400-100328200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
43	chr9:100324400-100329400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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