Variant report

Variant	rs1281350
Chromosome Location	chr9:18473576-18473577
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	PBX3	chr9:18473549-18475472	SK-N-SH	brain:	n/a	chr9:18474017-18474026
2	REST	chr9:18473495-18474578	H1-neurons	neurons:	n/a	n/a
3	GATA3	chr9:18473469-18475574	SK-N-SH	brain:	n/a	chr9:18475248-18475258 chr9:18475011-18475020 chr9:18474392-18474409
4	KAP1	chr9:18473565-18474599	HEK293	kidney:	n/a	n/a
5	TCF12	chr9:18473436-18475479	SK-N-SH	brain:	n/a	n/a
6	TCF12	chr9:18473562-18474612	SK-N-SH	brain:	n/a	n/a

Variant related genes	Relation type
ADAMTSL1	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10217409	0.82[EUR][1000 genomes]
rs10217753	0.96[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs10738510	0.81[ASN][1000 genomes]
rs10756964	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10810969	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs10810970	0.82[ASN][1000 genomes]
rs10810971	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10810973	0.80[ASN][1000 genomes]
rs11793923	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs1329721	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1340040	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1832747	0.92[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.80[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1888067	0.96[CEU][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2153415	0.86[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs2153416	0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap]
rs4961649	0.90[EUR][1000 genomes]
rs4961650	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4961651	0.80[ASN][1000 genomes]
rs4961652	0.82[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs4961653	0.96[CEU][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs4961654	0.88[CEU][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes]
rs6475216	0.88[EUR][1000 genomes]
rs6475219	0.81[ASN][1000 genomes]
rs7019399	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7856703	0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs7864856	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491807	chr9:18243672-19009770	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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	nsv525659	chr9:18288212-19009041	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer 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
3	nsv1019127	chr9:18288271-18996288	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh 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
4	nsv892688	chr9:18385143-18551247	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv1029449	chr9:18414752-18829127	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
6	nsv540077	chr9:18414752-18829127	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats 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 miRNA target site	5 gene(s)	inside rSNPs	diseases
7	nsv1030931	chr9:18414752-18903530	ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1281350	ADAMTSL1	cis	parietal	SCAN
rs1281350	CNTLN	cis	cerebellum	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:18464200-18474400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr9:18471800-18475800	Enhancers	Hela-S3	cervix
3	chr9:18472200-18473600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr9:18472200-18473800	Enhancers	NHEK	skin
5	chr9:18472400-18473600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr9:18472600-18473600	Enhancers	H9 Cell Line	embryonic stem cell
7	chr9:18472600-18473800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr9:18472800-18473600	Enhancers	Brain Anterior Caudate	brain
9	chr9:18472800-18473600	Enhancers	Colon Smooth Muscle	Colon
10	chr9:18472800-18473600	Flanking Active TSS	NH-A	brain
11	chr9:18472800-18473800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
12	chr9:18472800-18473800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr9:18472800-18474000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr9:18472800-18474000	Flanking Active TSS	Brain Germinal Matrix	brain
15	chr9:18473000-18473600	Enhancers	H1 Cell Line	embryonic stem cell
16	chr9:18473000-18473600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr9:18473000-18473600	Enhancers	iPS-15b Cell Line	embryonic stem cell
18	chr9:18473000-18473600	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr9:18473000-18473600	Enhancers	Right Atrium	heart
20	chr9:18473000-18473800	Flanking Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:18473000-18473800	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
22	chr9:18473000-18473800	Enhancers	Aorta	Aorta
23	chr9:18473000-18473800	Enhancers	Left Ventricle	heart
24	chr9:18473000-18473800	Enhancers	Ovary	ovary
25	chr9:18473000-18473800	Enhancers	Rectal Smooth Muscle	rectum
26	chr9:18473000-18473800	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr9:18473000-18474000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr9:18473000-18474000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
29	chr9:18473000-18474000	Enhancers	Esophagus	oesophagus
30	chr9:18473000-18474000	Flanking Active TSS	Osteobl	bone
31	chr9:18473000-18474200	Enhancers	Fetal Brain Male	brain
32	chr9:18473000-18474200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
33	chr9:18473000-18474600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
34	chr9:18473000-18475200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr9:18473000-18475200	Active TSS	Duodenum Smooth Muscle	Duodenum
36	chr9:18473000-18476800	Flanking Active TSS	HUVEC	blood vessel
37	chr9:18473000-18478000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr9:18473200-18473600	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr9:18473200-18473600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:18473200-18473600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr9:18473200-18473600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr9:18473200-18473600	Enhancers	Brain Hippocampus Middle	brain
43	chr9:18473200-18473600	Enhancers	Fetal Lung	lung
44	chr9:18473200-18473800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr9:18473200-18474600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
46	chr9:18473200-18476400	Active TSS	NHLF	lung
47	chr9:18473200-18476800	Active TSS	NHDF-Ad	bronchial
48	chr9:18473200-18477800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr9:18473200-18477800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr9:18473400-18473600	Weak transcription	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links