Variant report

Variant	rs2297180
Chromosome Location	chr9:117810158-117810159
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:117810151..117812770-chr9:117815287..117818009,2	K562	blood:

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10123436	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1060545	0.82[MKK][hapmap]
rs10759752	0.84[CEU][hapmap];0.87[EUR][1000 genomes]
rs10817705	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330363	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330364	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330368	0.82[MKK][hapmap]
rs1411456	0.86[JPT][hapmap]
rs1411461	0.86[JPT][hapmap]
rs1537017	0.86[JPT][hapmap]
rs1547691	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1547692	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1854707	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1888222	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2009023	0.91[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2104772	0.83[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs3789872	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs3789873	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs4460459	0.86[JPT][hapmap]
rs6478127	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6478128	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7030164	0.86[JPT][hapmap]
rs7875852	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs944223	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs944226	0.86[JPT][hapmap]
rs953288	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][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	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2297180	COL27A1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117792800-117815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr9:117799400-117817000	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
7	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
8	chr9:117801000-117812400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr9:117801000-117819200	Weak transcription	HMEC	breast
10	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
12	chr9:117802600-117812400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr9:117803400-117810400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:117803400-117812000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
16	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
19	chr9:117804600-117812800	Weak transcription	NHEK	skin
20	chr9:117805800-117818800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr9:117806800-117810600	Enhancers	Rectal Smooth Muscle	rectum
22	chr9:117806800-117816800	Strong transcription	Osteobl	bone
23	chr9:117807200-117816800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr9:117807400-117819600	Strong transcription	NHDF-Ad	bronchial
25	chr9:117807400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr9:117807600-117811400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr9:117807600-117817400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr9:117807800-117813800	Strong transcription	NH-A	brain
29	chr9:117808000-117810800	Genic enhancers	Colon Smooth Muscle	Colon
30	chr9:117808200-117810200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:117808200-117812400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
32	chr9:117808600-117810200	Enhancers	Fetal Lung	lung
33	chr9:117808600-117811200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:117808600-117815000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr9:117809000-117810200	Weak transcription	Stomach Smooth Muscle	stomach
36	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:117809200-117810200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
38	chr9:117809200-117813800	Strong transcription	Cortex derived primary cultured neurospheres	brain
39	chr9:117809200-117821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr9:117809400-117815000	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:117809800-117810800	Strong transcription	NHLF	lung
42	chr9:117809800-117815200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr9:117810000-117817600	Weak transcription	Fetal Stomach	stomach

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