Variant report

Variant	rs11253542
Chromosome Location	chr10:1016110-1016111
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr10:1014806..1016425-chr10:1022937..1025172,2	MCF-7	breast:
2	chr10:1013235..1016804-chr10:1032534..1035039,3	K562	blood:
3	chr10:1015043..1019353-chr10:1030351..1034278,6	MCF-7	breast:
4	chr10:1015182..1016794-chr10:1031895..1033943,2	K562	blood:
5	chr10:1014659..1017574-chr10:1040488..1045906,4	K562	blood:
6	chr10:1015085..1016586-chr10:1048514..1051399,2	MCF-7	breast:
7	chr10:993234..997786-chr10:1013619..1016483,4	MCF-7	breast:
8	chr10:978959..981256-chr10:1013885..1016544,2	K562	blood:
9	chr10:975132..982582-chr10:1010670..1022073,17	MCF-7	breast:
10	chr10:1009125..1012338-chr10:1015177..1017521,3	K562	blood:
11	chr10:1015119..1019104-chr10:1032459..1035516,7	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000107929	Chromatin interaction
ENSG00000107937	Chromatin interaction
ENSG00000229869	Chromatin interaction
ENSG00000205740	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10795304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10795305	1.00[CEU][hapmap];0.80[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10795307	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10904591	0.83[EUR][1000 genomes]
rs10904592	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10904593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11253516	0.89[CEU][hapmap]
rs11253526	0.83[CEU][hapmap]
rs11253527	0.89[CEU][hapmap]
rs11253543	1.00[CEU][hapmap];0.80[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11253544	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11253564	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11599792	0.83[JPT][hapmap]
rs12217202	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12268008	0.83[JPT][hapmap]
rs12355506	0.85[EUR][1000 genomes]
rs2170142	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2279257	0.94[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs2306404	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs2306406	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap]
rs2306408	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2892252	0.94[CEU][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2892253	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3765102	0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4880745	0.83[JPT][hapmap]
rs4881547	0.81[JPT][hapmap]
rs5027030	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7069123	0.83[JPT][hapmap]
rs7071250	0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7081516	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7082783	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7093767	0.88[CEU][hapmap]
rs7094916	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.86[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7097976	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7905827	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7915650	0.84[CEU][hapmap]
rs7917055	0.94[CEU][hapmap];0.90[CHB][hapmap];0.94[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7920922	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs947403	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916591	chr10:224406-1088734	Enhancers Weak transcription Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
2	nsv540386	chr10:224406-1197416	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
3	nsv1054659	chr10:611444-1133578	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
4	nsv466697	chr10:734229-1129527	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
5	nsv549765	chr10:734229-1129527	Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
6	nsv530116	chr10:776548-1401075	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
7	nsv948978	chr10:813426-1019115	Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1052540	chr10:887562-1300134	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
9	nsv540407	chr10:887562-1300134	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
10	nsv533861	chr10:945438-1382068	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
11	nsv530117	chr10:945438-1729634	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
12	nsv540408	chr10:955835-1260680	Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
13	nsv817532	chr10:964660-1885945	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
14	esv2753756	chr10:985264-1052950	Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv1050577	chr10:986723-1277854	Weak transcription Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
16	nsv540409	chr10:986723-1277854	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
17	nsv5521	chr10:986842-1031352	Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
18	nsv1037193	chr10:989533-1019630	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
19	nsv949405	chr10:1010464-1376105	Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
20	nsv525014	chr10:1013535-1024214	Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
21	nsv1048254	chr10:1016006-1146595	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11253542	WDR37	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:998800-1026200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr10:1007600-1016800	Weak transcription	Right Atrium	heart
3	chr10:1012400-1019000	Enhancers	Placenta	Placenta
4	chr10:1013400-1016800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr10:1013600-1018800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr10:1014200-1020600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr10:1014600-1018600	Weak transcription	Brain Angular Gyrus	brain
8	chr10:1014800-1022400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr10:1015000-1016600	Weak transcription	Duodenum Mucosa	Duodenum
10	chr10:1015200-1016200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr10:1015600-1016400	Enhancers	Fetal Lung	lung
12	chr10:1015600-1017200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr10:1015800-1016400	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr10:1015800-1016600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr10:1015800-1017000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr10:1015800-1018000	Enhancers	Pancreas	Pancrea
17	chr10:1015800-1018000	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr10:1015800-1018000	Flanking Active TSS	HepG2	liver
19	chr10:1015800-1019800	Enhancers	Pancreatic Islets	Pancreatic Islet
20	chr10:1016000-1016200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:1016000-1016200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr10:1016000-1016400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr10:1016000-1016400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr10:1016000-1016400	Enhancers	Adipose Nuclei	Adipose
25	chr10:1016000-1016400	Enhancers	A549	lung
26	chr10:1016000-1016400	Enhancers	Hela-S3	cervix
27	chr10:1016000-1016600	Weak transcription	Ovary	ovary
28	chr10:1016000-1016600	Enhancers	NHDF-Ad	bronchial
29	chr10:1016000-1016600	Enhancers	NHLF	lung
30	chr10:1016000-1016800	Enhancers	Liver	Liver
31	chr10:1016000-1016800	Weak transcription	Gastric	stomach
32	chr10:1016000-1016800	Bivalent Enhancer	K562	blood
33	chr10:1016000-1017400	Enhancers	Fetal Kidney	kidney
34	chr10:1016000-1017400	Enhancers	Fetal Stomach	stomach
35	chr10:1016000-1021600	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links