Variant report

Variant	rs2512478
Chromosome Location	chr11:86755553-86755554
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10792903	1.00[CHB][hapmap]
rs1378880	0.82[GIH][hapmap]
rs2124577	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2124579	1.00[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap]
rs2124581	0.82[MEX][hapmap]
rs2374996	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2445537	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445538	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2445543	0.84[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs2445549	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.87[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap]
rs2445552	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.81[ASN][1000 genomes]
rs2445564	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs2445565	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2445570	0.88[ASN][1000 genomes]
rs2445581	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs2512327	0.82[MEX][hapmap]
rs2512347	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes]
rs2512352	0.82[MEX][hapmap]
rs2512353	0.82[MEX][hapmap]
rs2512364	0.90[ASN][1000 genomes]
rs2512370	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2512371	0.97[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2512373	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2512378	0.84[JPT][hapmap]
rs2512379	0.88[ASN][1000 genomes]
rs2512382	0.81[MEX][hapmap]
rs2512390	0.82[MEX][hapmap]
rs2512392	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2512486	0.93[ASN][1000 genomes]
rs2512488	0.82[MEX][hapmap]
rs2512493	1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap]
rs2512498	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2512502	0.91[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs2513206	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2513207	0.82[MEX][hapmap]
rs2513219	0.89[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.88[ASN][1000 genomes]
rs2513220	0.88[ASN][1000 genomes]
rs2513225	0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.81[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2513232	0.87[GIH][hapmap];0.83[JPT][hapmap];0.81[TSI][hapmap]
rs2513234	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3740659	0.91[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs965467	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv1037042	chr11:86586876-86978492	Enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv541119	chr11:86586876-86978492	Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	esv13345	chr11:86753735-86756555	Weak transcription Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Genic enhancers	n/a	n/a	inside rSNPs	n/a
6	nsv898058	chr11:86754948-86889284	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv898059	chr11:86754948-86949369	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv1043562	chr11:86755535-87547185	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv541120	chr11:86755535-87547185	Bivalent Enhancer Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2512478	TMEM135	cis	parietal	SCAN
rs2512478	FZD4	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86749600-86758200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr11:86749600-86766800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr11:86750000-86756400	Weak transcription	Primary B cells from cord blood	blood
4	chr11:86750000-86765800	Weak transcription	Placenta	Placenta
5	chr11:86750400-86760600	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr11:86750600-86755600	Weak transcription	Fetal Intestine Small	intestine
7	chr11:86750600-86755600	Weak transcription	Right Ventricle	heart
8	chr11:86750600-86756400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:86750600-86757600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr11:86750600-86757800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr11:86750600-86757800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr11:86750600-86757800	Weak transcription	Fetal Intestine Large	intestine
13	chr11:86750600-86759800	Weak transcription	Fetal Thymus	thymus
14	chr11:86750600-86760600	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr11:86750800-86757200	Weak transcription	Fetal Muscle Leg	muscle
16	chr11:86750800-86757800	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr11:86750800-86758600	Weak transcription	HSMM	muscle
18	chr11:86750800-86759800	Weak transcription	HSMMtube	muscle
19	chr11:86750800-86760000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr11:86750800-86760200	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr11:86750800-86780600	Weak transcription	Primary T helper cells fromperipheralblood	blood
22	chr11:86750800-86782000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr11:86750800-86787400	Weak transcription	A549	lung
24	chr11:86751000-86757000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr11:86751000-86757400	Weak transcription	Stomach Smooth Muscle	stomach
26	chr11:86751000-86760000	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:86751000-86786800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr11:86751000-86787400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr11:86751200-86756200	Weak transcription	Duodenum Mucosa	Duodenum
30	chr11:86751200-86756600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr11:86751200-86757200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr11:86751200-86762600	Weak transcription	Primary T helper cells PMA-I stimulated	--
33	chr11:86751200-86785600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr11:86751400-86756600	Weak transcription	Hela-S3	cervix
35	chr11:86751400-86757400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr11:86751400-86758400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr11:86751400-86759800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr11:86751400-86767800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:86751400-86786400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr11:86751600-86757000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr11:86751600-86757400	Weak transcription	Fetal Lung	lung
42	chr11:86751600-86757800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr11:86751600-86787000	Weak transcription	Aorta	Aorta
44	chr11:86752000-86768800	Weak transcription	Ovary	ovary
45	chr11:86752000-86768800	Weak transcription	Psoas Muscle	Psoas
46	chr11:86752200-86756400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:86752200-86757600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
48	chr11:86752200-86759800	Weak transcription	Fetal Brain Male	brain
49	chr11:86752200-86768800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr11:86752400-86758200	Weak transcription	Brain Cingulate Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links