Variant report

Variant	rs7518399
Chromosome Location	chr1:212526013-212526014
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:212525375..212527593-chr1:212964320..212966298,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117697	Chromatin interaction
ENSG00000203705	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10494951	1.00[ASW][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap]
rs10863960	0.81[EUR][1000 genomes]
rs10863961	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs10863963	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11119919	0.94[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119920	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11119924	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11119929	0.84[ASN][1000 genomes]
rs11119930	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11576437	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap]
rs11576769	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11580285	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap]
rs11584189	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11585215	0.87[EUR][1000 genomes]
rs11587555	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588867	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589817	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs11590242	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.89[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11590672	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12060029	1.00[CHB][hapmap];0.94[CHD][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12062818	0.84[ASN][1000 genomes]
rs12073615	0.81[CHD][hapmap]
rs12090970	0.88[ASN][1000 genomes]
rs12095810	0.88[ASN][1000 genomes]
rs12096035	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12411213	0.88[ASN][1000 genomes]
rs12726409	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12727947	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.92[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap]
rs12728266	0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.86[TSI][hapmap]
rs12734895	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12737825	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12743785	0.94[CEU][hapmap];0.86[CHB][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12745269	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12756678	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1470390	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493600	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17018997	0.83[TSI][hapmap]
rs17721302	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2120770	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2297306	1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2358448	1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2358454	0.87[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28737261	0.83[AFR][1000 genomes]
rs2884465	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2884466	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34080686	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34447409	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35822123	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4951595	0.84[ASN][1000 genomes]
rs55814152	0.87[EUR][1000 genomes]
rs56104831	0.84[ASN][1000 genomes]
rs6661987	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6667199	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[EUR][1000 genomes]
rs6676208	0.86[TSI][hapmap]
rs6693849	1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6697910	0.83[TSI][hapmap]
rs71646158	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs72754339	0.84[ASN][1000 genomes]
rs7531219	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7533689	0.83[TSI][hapmap]
rs968531	0.87[EUR][1000 genomes]
rs968532	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs7518399	C1orf74	cis	parietal	SCAN
rs7518399	RP11-15I11.3	cis	Thyroid	GTEx
rs7518399	TMEM206	cis	parietal	SCAN
rs7518399	RP11-15I11.3	cis	lung	GTEx
rs7518399	RP11-15I11.3	cis	Nerve Tibial	GTEx
rs7518399	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212489600-212554800	Weak transcription	Small Intestine	intestine
2	chr1:212493800-212533400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr1:212498000-212526200	Weak transcription	Fetal Brain Male	brain
4	chr1:212500000-212540400	Weak transcription	Stomach Mucosa	stomach
5	chr1:212501000-212533600	Weak transcription	Fetal Heart	heart
6	chr1:212501400-212526200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr1:212501400-212540800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:212501800-212540800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
9	chr1:212502400-212528200	Weak transcription	Muscle Satellite Cultured Cells	--
10	chr1:212502600-212563400	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr1:212502600-212564600	Strong transcription	Monocytes-CD14+_RO01746	blood
12	chr1:212502800-212541400	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr1:212504000-212548600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr1:212504400-212537600	Weak transcription	Psoas Muscle	Psoas
15	chr1:212505200-212531400	Weak transcription	HMEC	breast
16	chr1:212505800-212533200	Weak transcription	NH-A	brain
17	chr1:212508200-212526400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr1:212508200-212528000	Weak transcription	Fetal Kidney	kidney
19	chr1:212508200-212545800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr1:212508600-212541000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:212511400-212540800	Strong transcription	Primary T cells fromperipheralblood	blood
22	chr1:212513200-212541000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr1:212513800-212540800	Strong transcription	Primary T helper cells fromperipheralblood	blood
24	chr1:212514400-212540400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr1:212514600-212537600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr1:212514800-212541800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:212515000-212527000	Strong transcription	Duodenum Mucosa	Duodenum
28	chr1:212515000-212528200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr1:212515000-212528400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr1:212515000-212528600	Strong transcription	Dnd41	blood
31	chr1:212515200-212536400	Strong transcription	Liver	Liver
32	chr1:212515400-212528600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr1:212516000-212528600	Strong transcription	Adipose Nuclei	Adipose
34	chr1:212516200-212528400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr1:212516600-212526200	Weak transcription	HSMMtube	muscle
36	chr1:212518000-212528000	Weak transcription	NHLF	lung
37	chr1:212518400-212531200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
38	chr1:212519200-212526600	Strong transcription	Primary hematopoietic stem cells	blood
39	chr1:212519200-212528200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr1:212520000-212528000	Weak transcription	Osteobl	bone
41	chr1:212520400-212526200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr1:212522200-212526200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr1:212522600-212529600	Weak transcription	NHDF-Ad	bronchial
44	chr1:212522800-212526200	Weak transcription	Fetal Lung	lung
45	chr1:212523400-212526400	Weak transcription	Hela-S3	cervix
46	chr1:212523600-212528000	Strong transcription	Fetal Intestine Small	intestine
47	chr1:212523600-212528200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
48	chr1:212523600-212550600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr1:212524000-212541800	Strong transcription	Fetal Thymus	thymus
50	chr1:212524400-212527200	Strong transcription	Cortex derived primary cultured neurospheres	brain

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