Variant report

Variant	rs2771040
Chromosome Location	chr9:108152199-108152200
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:108150925..108153260-chr9:108154410..108158072,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FSD1L-3	chr9:108152185-108153680	NONHSAT133813

Extended variants
information (count: 46 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10123494	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10491810	1.00[ASN][1000 genomes]
rs10820801	1.00[CEU][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10991629	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10991639	0.94[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.86[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12339823	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12340765	1.00[ASN][1000 genomes]
rs12342542	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12344130	0.90[YRI][hapmap];1.00[ASN][1000 genomes]
rs12350138	0.92[CEU][hapmap];0.81[EUR][1000 genomes]
rs13294525	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13294539	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410837	1.00[ASN][1000 genomes]
rs1410839	1.00[ASW][hapmap];1.00[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553870	1.00[ASN][1000 genomes]
rs1553873	1.00[ASN][1000 genomes]
rs16924529	1.00[ASN][1000 genomes]
rs16924530	0.90[YRI][hapmap];0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs17246524	1.00[ASN][1000 genomes]
rs17305886	1.00[ASN][1000 genomes]
rs17305963	1.00[ASN][1000 genomes]
rs2417615	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2771031	1.00[ASN][1000 genomes]
rs2771033	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812314	1.00[ASN][1000 genomes]
rs2812316	1.00[ASN][1000 genomes]
rs3199966	1.00[ASW][hapmap];1.00[MEX][hapmap];0.90[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34750132	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35603631	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41296093	1.00[ASN][1000 genomes]
rs4549843	0.84[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6479311	1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6479313	0.92[CEU][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6479314	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6479315	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6479316	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7024985	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7029443	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7045091	1.00[CEU][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs724069	1.00[ASN][1000 genomes]
rs7858401	1.00[ASN][1000 genomes]
rs7865985	1.00[CEU][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7873937	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs907230	1.00[CEU][hapmap];0.86[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045108	chr9:107509553-108188550	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1037750	chr9:108027692-108251733	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2771040	OR13F1	cis	parietal	SCAN
rs2771040	CYLC2	cis	parietal	SCAN
rs2771040	ZNF189	cis	cerebellum	SCAN
rs2771040	SLC44A1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:108096200-108164200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr9:108105000-108154800	Weak transcription	Small Intestine	intestine
3	chr9:108121600-108157000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr9:108122600-108153400	Weak transcription	Stomach Mucosa	stomach
5	chr9:108123600-108154400	Weak transcription	Colonic Mucosa	Colon
6	chr9:108125000-108166800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr9:108125600-108157000	Weak transcription	Osteobl	bone
8	chr9:108137800-108155400	Weak transcription	Lung	lung
9	chr9:108137800-108156200	Weak transcription	Fetal Stomach	stomach
10	chr9:108137800-108156400	Weak transcription	Aorta	Aorta
11	chr9:108137800-108157200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr9:108137800-108158200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr9:108138000-108156400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr9:108138000-108156400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr9:108138600-108153000	Weak transcription	Fetal Brain Female	brain
16	chr9:108143600-108157000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr9:108146800-108177600	Weak transcription	Left Ventricle	heart
18	chr9:108148000-108155200	Weak transcription	HSMM	muscle
19	chr9:108148200-108152200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr9:108148200-108153800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr9:108148200-108154000	Weak transcription	Fetal Intestine Small	intestine
22	chr9:108148200-108155800	Weak transcription	Adipose Nuclei	Adipose
23	chr9:108148200-108156200	Weak transcription	Rectal Smooth Muscle	rectum
24	chr9:108148200-108158800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr9:108148200-108158800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr9:108148200-108160200	Weak transcription	Ovary	ovary
27	chr9:108148400-108152200	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:108148400-108152800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr9:108148400-108153000	Weak transcription	Thymus	Thymus
30	chr9:108148400-108155400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr9:108148400-108155800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr9:108148400-108156200	Weak transcription	Primary T cells from cord blood	blood
33	chr9:108148400-108156600	Weak transcription	Primary hematopoietic stem cells	blood
34	chr9:108148400-108158600	Weak transcription	Fetal Lung	lung
35	chr9:108148400-108160400	Weak transcription	Fetal Intestine Large	intestine
36	chr9:108148400-108168000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr9:108148600-108152400	Weak transcription	Brain Anterior Caudate	brain
38	chr9:108148600-108158200	Weak transcription	Rectal Mucosa Donor 31	rectum
39	chr9:108148800-108165600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr9:108149000-108154800	Weak transcription	Liver	Liver
41	chr9:108149000-108155600	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr9:108149400-108153600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr9:108149600-108153600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr9:108149800-108154800	Weak transcription	Fetal Thymus	thymus
45	chr9:108149800-108155400	Strong transcription	Monocytes-CD14+_RO01746	blood
46	chr9:108150000-108156800	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:108150200-108152400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:108151000-108153800	Enhancers	Fetal Brain Male	brain
49	chr9:108151000-108154000	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr9:108151200-108155400	Enhancers	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links