Variant report

Variant	rs12418852
Chromosome Location	chr11:47868853-47868854
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:47792091..47794821-chr11:47867403..47869086,2	K562	blood:
2	chr11:47734421..47738084-chr11:47868728..47871724,4	K562	blood:
3	chr11:47787394..47789838-chr11:47868299..47871448,5	MCF-7	breast:
4	chr11:47597915..47601799-chr11:47868286..47871887,4	K562	blood:
5	chr11:47787149..47790720-chr11:47868235..47871590,6	MCF-7	breast:
6	chr11:47788106..47790225-chr11:47868385..47869954,2	K562	blood:
7	chr11:47735300..47737622-chr11:47868024..47869979,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200376	Chromatin interaction
ENSG00000231880	Chromatin interaction
ENSG00000123444	Chromatin interaction
ENSG00000109920	Chromatin interaction
ENSG00000165923	Chromatin interaction
ENSG00000213619	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10838747	1.00[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs10838748	1.00[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs10838757	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11039355	0.81[ASN][1000 genomes]
rs11039389	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11039390	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039391	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11039416	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039426	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11039433	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11602339	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11605774	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12361031	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12361256	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12364432	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12421210	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12785833	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12787112	1.00[CEU][hapmap];0.86[CHB][hapmap];0.87[JPT][hapmap]
rs12787330	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12798109	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12803191	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17788930	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2290850	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34128973	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34614231	0.84[AMR][1000 genomes]
rs34910028	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34923397	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35805829	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35902101	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35985502	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752797	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752801	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4752873	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7105282	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7120333	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7130758	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7927771	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7947730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1052397	chr11:47675470-48594256	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv832143	chr11:47700808-47883540	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
3	nsv530620	chr11:47765455-48664555	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
4	nsv1036992	chr11:47794621-48666024	Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv1049835	chr11:47837089-47928822	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv541036	chr11:47837089-47928822	Enhancers Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12418852	C1QTNF4	cis	multi-tissue	Pritchard
rs12418852	C1QTNF4	cis	Adipose Subcutaneous	GTEx
rs12418852	C1QTNF4	cis	Skin Sun Exposed Lower leg	GTEx
rs12418852	NDUFS3	Cis_1M	lymphoblastoid	RTeQTL
rs12418852		cis	Lymphoblastoid	GTEx
rs12418852	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs12418852	SPI1	cis	multi-tissue	Pritchard
rs12418852	Hs.6637	cis	multi-tissue	Pritchard
rs12418852	C1QTNF4	cis	lung	GTEx
rs12418852	C1QTNF4	cis	Whole Blood	GTEx
rs12418852	C1QTNF4	cis	Muscle Skeletal	GTEx
rs12418852	C1QTNF4	cis	Esophagus Mucosa	GTEx
rs12418852	SPI1	cis	Lymphoblastoid	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47790200-47869200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47856600-47869200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr11:47865000-47869200	Weak transcription	Gastric	stomach
4	chr11:47865400-47869200	Weak transcription	Aorta	Aorta
5	chr11:47865800-47869400	Weak transcription	Spleen	Spleen
6	chr11:47866000-47869200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr11:47866000-47869200	Weak transcription	Esophagus	oesophagus
8	chr11:47866400-47869000	Weak transcription	Right Ventricle	heart
9	chr11:47866400-47869200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr11:47866600-47869200	Weak transcription	Left Ventricle	heart
11	chr11:47867200-47869200	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr11:47867200-47869200	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr11:47867400-47869000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr11:47867600-47869200	Enhancers	Primary T cells fromperipheralblood	blood
15	chr11:47867600-47869200	Weak transcription	Lung	lung
16	chr11:47867600-47869200	Weak transcription	Ovary	ovary
17	chr11:47867600-47869400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr11:47867800-47869200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
19	chr11:47868000-47869000	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr11:47868000-47869000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr11:47868000-47869000	Enhancers	Liver	Liver
22	chr11:47868000-47869000	Transcr. at gene 5' and 3'	Dnd41	blood
23	chr11:47868000-47869000	Genic enhancers	HSMMtube	muscle
24	chr11:47868000-47869200	Enhancers	Brain Substantia Nigra	brain
25	chr11:47868200-47869000	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
26	chr11:47868200-47869000	Flanking Active TSS	GM12878-XiMat	blood
27	chr11:47868200-47869200	Transcr. at gene 5' and 3'	Hela-S3	cervix
28	chr11:47868200-47869200	Flanking Active TSS	HepG2	liver
29	chr11:47868200-47870400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr11:47868400-47869000	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:47868400-47869000	Transcr. at gene 5' and 3'	iPS-18 Cell Line	embryonic stem cell
32	chr11:47868400-47869000	Enhancers	Primary T cells from cord blood	blood
33	chr11:47868400-47869000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr11:47868400-47869000	Enhancers	Adipose Nuclei	Adipose
35	chr11:47868400-47869000	Enhancers	Brain Anterior Caudate	brain
36	chr11:47868400-47869000	Enhancers	Small Intestine	intestine
37	chr11:47868400-47869000	Transcr. at gene 5' and 3'	K562	blood
38	chr11:47868400-47869200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr11:47868400-47869200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr11:47868400-47869400	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr11:47868400-47869600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr11:47868400-47869600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
43	chr11:47868600-47869000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
44	chr11:47868600-47869000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
45	chr11:47868600-47869000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:47868600-47869000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr11:47868600-47869000	Enhancers	Brain Hippocampus Middle	brain
48	chr11:47868600-47869000	Enhancers	Colonic Mucosa	Colon
49	chr11:47868600-47869000	Genic enhancers	Fetal Muscle Leg	muscle
50	chr11:47868600-47869000	Genic enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links