Variant report

Variant	rs9588117
Chromosome Location	chr13:110860343-110860344
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10492498	0.91[CEU][hapmap];1.00[JPT][hapmap];0.80[TSI][hapmap];0.85[EUR][1000 genomes]
rs12867220	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12868210	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12869358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12869391	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12873869	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12874407	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1373749	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1981317	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1982315	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35345744	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35784668	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4773131	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4773132	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs490727	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs61964980	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs665713	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs685884	0.95[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs686746	0.95[CEU][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes]
rs687617	0.81[EUR][1000 genomes]
rs7331702	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332235	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7333008	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7994305	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs7996767	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7996925	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9515163	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs9515165	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9515166	0.91[CEU][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9521642	0.82[CEU][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs9521644	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9521646	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9521649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9583467	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs995223	0.91[CEU][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes]
rs995224	0.83[AMR][1000 genomes];0.85[EUR][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	nsv1052147	chr13:110765635-110917782	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
2	nsv1182	chr13:110829691-110875029	Strong transcription Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
3	nsv1038914	chr13:110860219-111190104	Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9588117	COL4A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:110791400-110868400	Weak transcription	Psoas Muscle	Psoas
2	chr13:110806600-110860400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr13:110810200-110866400	Strong transcription	Stomach Smooth Muscle	stomach
4	chr13:110826400-110868200	Weak transcription	Brain Cingulate Gyrus	brain
5	chr13:110826600-110866200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:110826800-110868000	Weak transcription	Brain Anterior Caudate	brain
7	chr13:110827600-110869000	Weak transcription	Brain Hippocampus Middle	brain
8	chr13:110829000-110865000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr13:110829600-110874400	Weak transcription	A549	lung
10	chr13:110829800-110869600	Weak transcription	Small Intestine	intestine
11	chr13:110830000-110870800	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr13:110830200-110869600	Weak transcription	Fetal Brain Male	brain
13	chr13:110831000-110866000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr13:110835400-110866800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr13:110836400-110874200	Weak transcription	Esophagus	oesophagus
16	chr13:110840800-110870200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr13:110841000-110868200	Weak transcription	NHDF-Ad	bronchial
18	chr13:110841200-110865600	Strong transcription	Muscle Satellite Cultured Cells	--
19	chr13:110841200-110866000	Strong transcription	NH-A	brain
20	chr13:110841200-110866400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr13:110841200-110868200	Weak transcription	Right Atrium	heart
22	chr13:110841400-110867800	Strong transcription	Osteobl	bone
23	chr13:110841800-110863600	Strong transcription	Fetal Muscle Trunk	muscle
24	chr13:110844600-110866200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
25	chr13:110845400-110865800	Strong transcription	Adipose Nuclei	Adipose
26	chr13:110846400-110869000	Weak transcription	Sigmoid Colon	Sigmoid Colon
27	chr13:110846400-110879800	Weak transcription	Pancreas	Pancrea
28	chr13:110847200-110864800	Weak transcription	Colonic Mucosa	Colon
29	chr13:110850200-110868000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr13:110850400-110862800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr13:110850600-110866200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:110852000-110863800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr13:110852000-110868200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr13:110852000-110869800	Weak transcription	Brain Germinal Matrix	brain
35	chr13:110852600-110862000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr13:110853000-110866200	Strong transcription	Placenta	Placenta
37	chr13:110853200-110864200	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr13:110853400-110866000	Weak transcription	Fetal Heart	heart
39	chr13:110853400-110868200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr13:110853600-110866000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr13:110853600-110879800	Weak transcription	Gastric	stomach
42	chr13:110854000-110868000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr13:110854400-110861600	Weak transcription	Rectal Smooth Muscle	rectum
44	chr13:110855400-110866400	Strong transcription	Colon Smooth Muscle	Colon
45	chr13:110855800-110865400	Strong transcription	HUES64 Cell Line	embryonic stem cell
46	chr13:110855800-110866400	Strong transcription	HSMMtube	muscle
47	chr13:110855800-110866400	Strong transcription	HUVEC	blood vessel
48	chr13:110856600-110865400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr13:110856800-110865600	Strong transcription	Duodenum Smooth Muscle	Duodenum
50	chr13:110856800-110866000	Strong transcription	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links