Variant report

Variant	rs1474056
Chromosome Location	chr11:47632707-47632708
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47573161..47575432-chr11:47631210..47633964,2	MCF-7	breast:
2	chr11:47599509..47601986-chr11:47631255..47633336,2	K562	blood:
3	chr11:47628145..47629992-chr11:47630122..47633055,2	MCF-7	breast:
4	chr11:47625880..47627610-chr11:47631920..47634659,2	K562	blood:
5	chr11:47625710..47627610-chr11:47631775..47635151,4	K562	blood:
6	chr11:47628108..47630703-chr11:47631634..47634626,3	K562	blood:
7	chr11:47631158..47632846-chr11:47873541..47876421,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000149187	Chromatin interaction
ENSG00000213619	Chromatin interaction
ENSG00000123444	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1044269	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap]
rs10742805	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs10742806	0.94[JPT][hapmap]
rs10742816	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11039300	0.87[EUR][1000 genomes]
rs11039387	0.80[ASN][1000 genomes]
rs11819955	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs11819979	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11820480	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12419342	0.94[JPT][hapmap]
rs17198158	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs17790804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17791016	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2138767	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242511	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2305982	0.80[ASN][1000 genomes]
rs2305983	0.80[ASN][1000 genomes]
rs2869531	0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2869532	0.87[ASN][1000 genomes]
rs3740684	0.92[GIH][hapmap];0.89[JPT][hapmap]
rs3824867	0.88[GIH][hapmap];0.94[JPT][hapmap]
rs3847503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap]
rs4147730	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4237544	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs4282946	0.94[JPT][hapmap]
rs4752783	1.00[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]
rs4752786	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4752791	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.84[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752837	0.94[JPT][hapmap]
rs4752839	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[CHD][hapmap];0.92[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap]
rs4752842	0.82[MEX][hapmap]
rs4752843	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs4752848	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4752871	0.80[ASN][1000 genomes]
rs4752872	0.80[ASN][1000 genomes]
rs4752877	0.80[ASN][1000 genomes]
rs56836683	0.82[AFR][1000 genomes]
rs57436966	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs57828885	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58119589	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs58357937	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59205786	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs59837204	0.84[EUR][1000 genomes]
rs60515486	0.85[ASN][1000 genomes]
rs6485772	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6485774	0.95[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs6485783	0.92[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];0.94[TSI][hapmap];0.82[ASN][1000 genomes]
rs6485784	0.80[ASN][1000 genomes]
rs6485788	0.80[ASN][1000 genomes]
rs7105122	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7105907	0.94[JPT][hapmap]
rs7111873	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7116299	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7120737	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7121264	0.85[ASN][1000 genomes]
rs7124949	0.80[ASN][1000 genomes]
rs7126210	0.92[GIH][hapmap];0.94[JPT][hapmap]
rs7927611	0.80[ASN][1000 genomes]
rs7931089	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935802	0.85[AFR][1000 genomes]
rs7939069	0.92[ASW][hapmap];0.96[LWK][hapmap];0.83[MKK][hapmap];0.84[YRI][hapmap]
rs7942031	0.80[ASN][1000 genomes]
rs7944532	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7945911	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7948705	0.94[JPT][hapmap]
rs7952204	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9666924	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap]

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	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1474056	SLC35C1	cis	cerebellum	SCAN
rs1474056	LOC441601	cis	cerebellum	SCAN
rs1474056	ATG13	cis	parietal	SCAN

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47607000-47632800	Weak transcription	Dnd41	blood
2	chr11:47617600-47643200	Weak transcription	Rectal Smooth Muscle	rectum
3	chr11:47618000-47639200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr11:47620800-47637800	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:47621000-47640400	Weak transcription	Fetal Brain Female	brain
6	chr11:47621600-47638200	Weak transcription	Hela-S3	cervix
7	chr11:47621600-47647600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr11:47621800-47642000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:47622000-47636000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr11:47622000-47637600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:47623000-47632800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr11:47625200-47637800	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr11:47626000-47632800	Weak transcription	Psoas Muscle	Psoas
14	chr11:47626000-47638400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
15	chr11:47626200-47638400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:47626400-47639200	Weak transcription	Colonic Mucosa	Colon
17	chr11:47626600-47635000	Weak transcription	A549	lung
18	chr11:47626600-47639000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr11:47627800-47643200	Weak transcription	Pancreas	Pancrea
20	chr11:47628600-47638400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr11:47628600-47638600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr11:47628800-47642000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr11:47629200-47638000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr11:47629400-47638400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:47629400-47639600	Weak transcription	HMEC	breast
26	chr11:47629800-47634800	Weak transcription	Brain Anterior Caudate	brain
27	chr11:47629800-47636600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr11:47629800-47637800	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr11:47629800-47638600	Weak transcription	Brain Angular Gyrus	brain
30	chr11:47629800-47640800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr11:47629800-47642400	Weak transcription	Colon Smooth Muscle	Colon
32	chr11:47630000-47634800	Weak transcription	Brain Hippocampus Middle	brain
33	chr11:47630000-47634800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr11:47630000-47638400	Weak transcription	Thymus	Thymus
35	chr11:47630000-47638400	Weak transcription	Osteobl	bone
36	chr11:47630000-47639000	Weak transcription	NHLF	lung
37	chr11:47630000-47639800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr11:47630000-47641200	Weak transcription	Small Intestine	intestine
39	chr11:47630000-47642200	Weak transcription	Fetal Brain Male	brain
40	chr11:47630200-47632800	Weak transcription	HSMMtube	muscle
41	chr11:47630200-47633000	Weak transcription	Right Ventricle	heart
42	chr11:47630200-47638400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:47630200-47638600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:47630200-47638600	Weak transcription	NH-A	brain
45	chr11:47630200-47639200	Weak transcription	Placenta	Placenta
46	chr11:47630200-47639600	Weak transcription	Fetal Muscle Trunk	muscle
47	chr11:47630200-47640200	Weak transcription	HSMM	muscle
48	chr11:47630400-47638000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr11:47630400-47638800	Weak transcription	Muscle Satellite Cultured Cells	--
50	chr11:47630400-47648600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links