Variant report

Variant	rs11102562
Chromosome Location	chr1:113448853-113448854
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113446003..113448854-chr1:113463781..113465733,2	MCF-7	breast:
2	chr1:113447709..113449566-chr1:113450371..113452210,2	K562	blood:
3	chr1:113441801..113445545-chr1:113447072..113449494,3	K562	blood:
4	chr1:113448232..113450362-chr1:113454684..113457292,4	K562	blood:

Variant related genes	Relation type
ENSG00000155380	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10399593	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1049434	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs10776763	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857980	0.83[YRI][hapmap]
rs10857981	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10857982	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10857983	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102559	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11102565	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11102568	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12028967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12037621	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12043035	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1344429	0.90[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1539625	1.00[CEU][hapmap];0.89[GIH][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1629027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs17030905	0.91[GIH][hapmap]
rs2002402	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2360009	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3789592	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3889656	0.82[CEU][hapmap]
rs4301628	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[MKK][hapmap];0.97[TSI][hapmap];0.81[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4839273	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.94[YRI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57549167	0.93[EUR][1000 genomes]
rs61819971	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61819997	0.93[EUR][1000 genomes]
rs6537764	0.89[ASN][1000 genomes]
rs6537765	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6663872	0.87[ASN][1000 genomes]
rs6682142	0.98[EUR][1000 genomes]
rs7169	1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs7551223	0.91[ASN][1000 genomes]
rs7556664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs9787311	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS 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	68 gene(s)	inside rSNPs	diseases
9	nsv1004102	chr1:113295805-113551210	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
10	esv3399982	chr1:113358580-113542255	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
11	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS 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	69 gene(s)	inside rSNPs	diseases
12	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	esv3362439	chr1:113376621-113450321	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11102562	LRIG2	cis	parietal	SCAN
rs11102562	DENND2C	cis	parietal	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113439200-113459200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:113439200-113460400	Weak transcription	Aorta	Aorta
3	chr1:113440200-113456400	Weak transcription	Primary hematopoietic stem cells	blood
4	chr1:113440400-113459600	Weak transcription	Primary T cells from cord blood	blood
5	chr1:113443800-113449600	Enhancers	Stomach Mucosa	stomach
6	chr1:113444400-113454400	Weak transcription	HepG2	liver
7	chr1:113444400-113456600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr1:113445000-113450400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr1:113445600-113449400	Enhancers	HMEC	breast
10	chr1:113445800-113449200	Enhancers	H1 Cell Line	embryonic stem cell
11	chr1:113445800-113449600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr1:113445800-113449600	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr1:113445800-113450000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr1:113445800-113450400	Enhancers	Brain Hippocampus Middle	brain
15	chr1:113446000-113449000	Enhancers	Right Atrium	heart
16	chr1:113446000-113449600	Enhancers	Hela-S3	cervix
17	chr1:113446000-113450600	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:113446000-113456600	Weak transcription	Fetal Heart	heart
19	chr1:113446200-113449000	Enhancers	NHLF	lung
20	chr1:113446200-113449200	Enhancers	NH-A	brain
21	chr1:113446200-113449600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr1:113446200-113449600	Enhancers	Osteobl	bone
23	chr1:113446200-113455600	Weak transcription	A549	lung
24	chr1:113446400-113449600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:113446400-113449600	Enhancers	Muscle Satellite Cultured Cells	--
26	chr1:113446400-113450000	Weak transcription	Gastric	stomach
27	chr1:113446400-113457800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr1:113446600-113449000	Enhancers	Fetal Lung	lung
29	chr1:113446600-113449600	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr1:113446600-113459600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:113446800-113450000	Enhancers	HUVEC	blood vessel
32	chr1:113446800-113459800	Weak transcription	Psoas Muscle	Psoas
33	chr1:113447000-113449600	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr1:113447000-113452800	Weak transcription	Stomach Smooth Muscle	stomach
35	chr1:113447000-113454600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr1:113447200-113450600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr1:113447200-113455400	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr1:113447200-113456000	Weak transcription	Primary T helper cells PMA-I stimulated	--
39	chr1:113447200-113456400	Weak transcription	Sigmoid Colon	Sigmoid Colon
40	chr1:113447400-113449000	Enhancers	HSMM	muscle
41	chr1:113447400-113449000	Flanking Active TSS	NHEK	skin
42	chr1:113447400-113449200	Enhancers	Liver	Liver
43	chr1:113447400-113449600	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr1:113447400-113449600	Enhancers	Adipose Nuclei	Adipose
45	chr1:113447400-113449800	Enhancers	iPS-18 Cell Line	embryonic stem cell
46	chr1:113447400-113452600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr1:113447400-113459200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr1:113447400-113459600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
49	chr1:113447600-113449000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr1:113447600-113449000	Enhancers	H9 Cell Line	embryonic stem cell

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