Variant report

Variant	rs10985395
Chromosome Location	chr9:100961093-100961094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100959852..100962338-chr9:101552599..101554249,2	K562	blood:
2	chr9:100960639..100963416-chr9:100964074..100967407,4	K562	blood:
3	chr9:100954360..100957375-chr9:100960108..100963895,4	K562	blood:
4	chr9:100959996..100962412-chr9:101015683..101018543,2	K562	blood:
5	chr9:100946651..100948622-chr9:100960430..100962165,2	K562	blood:
6	chr9:100954612..100957574-chr9:100959524..100962967,5	K562	blood:

Variant related genes	Relation type
ENSG00000106789	Chromatin interaction
ENSG00000095383	Chromatin interaction
ENSG00000165138	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10046819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10217245	0.96[AMR][1000 genomes]
rs10217347	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217398	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10217458	0.96[AMR][1000 genomes]
rs10818608	1.00[AMR][1000 genomes]
rs10985391	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10985425	1.00[AMR][1000 genomes]
rs12339078	1.00[AMR][1000 genomes]
rs12342843	1.00[AMR][1000 genomes]
rs12342968	1.00[AMR][1000 genomes]
rs12345418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12346761	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12347046	0.82[AMR][1000 genomes]
rs12348326	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12352986	1.00[AMR][1000 genomes]
rs12551524	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12554925	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41283618	0.82[AMR][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	nsv1053729	chr9:100909554-100997718	Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv520067	chr9:100927161-100978542	Genic enhancers Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv430085	chr9:100928245-101339645	Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv831663	chr9:100941048-101109492	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	nsv1045780	chr9:100943318-101080389	Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	nsv540180	chr9:100943318-101080389	Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10985395	NANS	cis	parietal	SCAN
rs10985395	TBC1D2	cis	multi-tissue	Pritchard

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100955800-100961400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr9:100955800-100961400	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100955800-100961400	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr9:100955800-100961400	Weak transcription	Thymus	Thymus
5	chr9:100955800-100961600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr9:100955800-100961600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr9:100955800-100962000	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr9:100955800-100962000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:100955800-100962000	Weak transcription	HSMM	muscle
10	chr9:100955800-100964200	Weak transcription	Pancreas	Pancrea
11	chr9:100955800-100965200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr9:100955800-100965200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr9:100955800-100970400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr9:100955800-100970400	Weak transcription	Left Ventricle	heart
15	chr9:100955800-100970400	Weak transcription	Rectal Smooth Muscle	rectum
16	chr9:100955800-100970600	Weak transcription	Ovary	ovary
17	chr9:100955800-100970600	Weak transcription	Right Ventricle	heart
18	chr9:100955800-100975000	Weak transcription	Primary B cells from cord blood	blood
19	chr9:100955800-100975000	Weak transcription	NHDF-Ad	bronchial
20	chr9:100955800-100975200	Weak transcription	NH-A	brain
21	chr9:100955800-100975600	Weak transcription	Skeletal Muscle Female	skeletal muscle
22	chr9:100955800-101003200	Weak transcription	Primary hematopoietic stem cells	blood
23	chr9:100956000-100961200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr9:100956000-100961400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:100956000-100961400	Weak transcription	Duodenum Mucosa	Duodenum
26	chr9:100956000-100961400	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr9:100956000-100961600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr9:100956000-100961600	Weak transcription	NHLF	lung
29	chr9:100956000-100962000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:100956000-100965000	Weak transcription	Adipose Nuclei	Adipose
31	chr9:100956000-100969800	Weak transcription	Primary T cells from cord blood	blood
32	chr9:100956000-100970000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr9:100956000-100970600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr9:100956000-100971000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr9:100956000-100981000	Weak transcription	A549	lung
36	chr9:100956200-100961200	Weak transcription	Brain Anterior Caudate	brain
37	chr9:100956200-100961200	Weak transcription	Fetal Intestine Large	intestine
38	chr9:100956200-100961200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr9:100956200-100961800	Weak transcription	Hela-S3	cervix
40	chr9:100956200-100962000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr9:100956200-100964600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
42	chr9:100956200-100967800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr9:100956200-100967800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr9:100956200-100967800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
45	chr9:100956200-100968000	Weak transcription	Stomach Mucosa	stomach
46	chr9:100956200-100970000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr9:100956200-100973000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr9:100956400-100961400	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr9:100957000-100967800	Strong transcription	Fetal Intestine Small	intestine
50	chr9:100957200-100964400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links