Variant report

Variant	rs3815252
Chromosome Location	chr7:108119419-108119420
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:108114847..108116540-chr7:108118255..108119786,2	K562	blood:
2	chr7:108118558..108121444-chr7:108121859..108124782,2	K562	blood:
3	chr7:108108975..108111125-chr7:108118694..108120937,2	K562	blood:

Extended variants
information (count: 45 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10225561	0.83[CHB][hapmap]
rs10273997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10278246	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1034825	0.85[CEU][hapmap];0.83[CHB][hapmap]
rs1034829	0.85[CEU][hapmap];0.83[CHB][hapmap];0.82[EUR][1000 genomes]
rs13221639	0.89[TSI][hapmap]
rs13244602	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1473131	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17339110	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1859769	0.91[EUR][1000 genomes]
rs1859771	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1859772	1.00[CEU][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1859773	0.83[CHB][hapmap]
rs1859774	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1859775	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs194585	0.92[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs194586	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2074752	0.83[ASN][1000 genomes]
rs2214916	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2284291	0.85[CEU][hapmap];0.83[CHB][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes]
rs2284292	0.83[EUR][1000 genomes]
rs2300053	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs2396001	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3763462	0.96[CEU][hapmap];0.87[CHB][hapmap];0.85[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs40846	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs40849	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs40856	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs40890	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs40892	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs40903	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs40916	0.83[YRI][hapmap]
rs40922	0.85[YRI][hapmap]
rs6466239	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6466240	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6966431	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6976478	0.86[EUR][1000 genomes]
rs726471	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73426110	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7800334	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7806223	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs917251	0.85[CEU][hapmap];0.83[CHB][hapmap];0.83[EUR][1000 genomes]
rs9640707	1.00[CEU][hapmap];1.00[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];1.00[ASN][1000 genomes]
rs9785006	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[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	esv3348839	chr7:107377311-108286538	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Active TSS 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 target site	91 gene(s)	inside rSNPs	diseases
2	esv2753284	chr7:108105345-108130214	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3815252	NRCAM	cis	parietal	SCAN
rs3815252	LHFPL3	cis	parietal	SCAN
rs3815252	C7orf66	cis	cerebellum	SCAN

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:108098200-108140600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr7:108102400-108129600	Weak transcription	Pancreas	Pancrea
3	chr7:108102400-108137000	Weak transcription	NH-A	brain
4	chr7:108102400-108143600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr7:108102800-108126400	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr7:108102800-108158400	Weak transcription	HSMMtube	muscle
7	chr7:108105800-108158000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr7:108106200-108150800	Weak transcription	NHLF	lung
9	chr7:108106600-108127600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr7:108106800-108130000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr7:108107600-108141000	Weak transcription	Spleen	Spleen
12	chr7:108108600-108122000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr7:108109000-108126400	Weak transcription	HUVEC	blood vessel
14	chr7:108109000-108129000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr7:108109000-108136400	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr7:108109000-108141400	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr7:108109000-108162400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr7:108109600-108127600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr7:108109600-108140600	Weak transcription	Esophagus	oesophagus
20	chr7:108109600-108143400	Weak transcription	GM12878-XiMat	blood
21	chr7:108110200-108127800	Weak transcription	Fetal Brain Female	brain
22	chr7:108110800-108121000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr7:108111000-108137800	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr7:108111400-108142200	Strong transcription	Liver	Liver
25	chr7:108111400-108154800	Weak transcription	NHEK	skin
26	chr7:108111600-108138400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr7:108111600-108142600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr7:108111800-108143600	Strong transcription	Primary monocytes fromperipheralblood	blood
29	chr7:108113200-108122200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr7:108113200-108157000	Weak transcription	Psoas Muscle	Psoas
31	chr7:108113600-108129800	Weak transcription	Hela-S3	cervix
32	chr7:108113600-108140000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr7:108113800-108150800	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr7:108113800-108165800	Weak transcription	Gastric	stomach
35	chr7:108114000-108129800	Weak transcription	Fetal Heart	heart
36	chr7:108114000-108139800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr7:108114000-108165000	Weak transcription	Colonic Mucosa	Colon
38	chr7:108114400-108160000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr7:108114600-108132000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr7:108114800-108122000	Strong transcription	Adipose Nuclei	Adipose
41	chr7:108114800-108122000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr7:108114800-108134800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr7:108115000-108122000	Strong transcription	Primary B cells from cord blood	blood
44	chr7:108115200-108119800	Strong transcription	Primary neutrophils fromperipheralblood	blood
45	chr7:108115200-108151800	Weak transcription	NHDF-Ad	bronchial
46	chr7:108115400-108119600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr7:108115800-108132000	Weak transcription	A549	lung
48	chr7:108116000-108120000	Strong transcription	Primary T cells fromperipheralblood	blood
49	chr7:108116000-108122600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr7:108116000-108125800	Strong transcription	Primary B cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links