Variant report

Variant	rs12037621
Chromosome Location	chr1:113449627-113449628
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113448950..113451242-chr1:113537407..113540142,2	MCF-7	breast:
2	chr1:113448862..113452902-chr1:113455376..113458880,4	K562	blood:
3	chr1:113449050..113451234-chr1:113459095..113461088,2	K562	blood:
4	chr1:113448893..113450506-chr1:113473671..113476266,2	K562	blood:
5	chr1:113448232..113450362-chr1:113454684..113457292,4	K562	blood:

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

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

rs_ID	r²[population]
rs10399593	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1049434	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10776763	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857980	0.83[YRI][hapmap]
rs10857981	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10857982	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10857983	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11102559	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11102562	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];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102565	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11102568	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12028967	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12043035	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1344429	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1539625	1.00[CEU][hapmap];0.91[GIH][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1629027	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs17030905	0.93[GIH][hapmap];0.82[TSI][hapmap]
rs2002402	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2360009	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3789592	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs3889656	0.82[CEU][hapmap]
rs4301628	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.81[YRI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4839273	0.83[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.94[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57549167	0.93[EUR][1000 genomes]
rs61819971	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61819997	0.93[EUR][1000 genomes]
rs6537764	0.90[ASN][1000 genomes]
rs6537765	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6663872	0.88[ASN][1000 genomes]
rs6682142	0.98[EUR][1000 genomes]
rs7169	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs7551223	0.92[ASN][1000 genomes]
rs7556664	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[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
rs12037621	LRIG2	cis	parietal	SCAN
rs12037621	DENND2C	cis	parietal	SCAN

Chromatin state (count:105 , 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	chr1:113444400-113454400	Weak transcription	HepG2	liver
6	chr1:113444400-113456600	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr1:113445000-113450400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr1:113445800-113450000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr1:113445800-113450400	Enhancers	Brain Hippocampus Middle	brain
10	chr1:113446000-113450600	Enhancers	HUES48 Cell Line	embryonic stem cell
11	chr1:113446000-113456600	Weak transcription	Fetal Heart	heart
12	chr1:113446200-113455600	Weak transcription	A549	lung
13	chr1:113446400-113450000	Weak transcription	Gastric	stomach
14	chr1:113446400-113457800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:113446600-113459600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:113446800-113450000	Enhancers	HUVEC	blood vessel
17	chr1:113446800-113459800	Weak transcription	Psoas Muscle	Psoas
18	chr1:113447000-113452800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr1:113447000-113454600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr1:113447200-113450600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr1:113447200-113455400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr1:113447200-113456000	Weak transcription	Primary T helper cells PMA-I stimulated	--
23	chr1:113447200-113456400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr1:113447400-113449800	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr1:113447400-113452600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr1:113447400-113459200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr1:113447400-113459600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr1:113447600-113456200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr1:113447800-113452400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr1:113447800-113457800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr1:113447800-113458000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr1:113447800-113459600	Weak transcription	Colon Smooth Muscle	Colon
33	chr1:113447800-113470200	Weak transcription	Fetal Kidney	kidney
34	chr1:113448000-113449800	Enhancers	Brain Anterior Caudate	brain
35	chr1:113448000-113450000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr1:113448200-113450000	Enhancers	Brain Inferior Temporal Lobe	brain
37	chr1:113448200-113457800	Weak transcription	Ovary	ovary
38	chr1:113448400-113457800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:113448600-113450400	Enhancers	Brain Substantia Nigra	brain
40	chr1:113448600-113452800	Weak transcription	Dnd41	blood
41	chr1:113448600-113457600	Weak transcription	NHDF-Ad	bronchial
42	chr1:113448800-113449800	Enhancers	Fetal Intestine Small	intestine
43	chr1:113448800-113452600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr1:113448800-113454400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr1:113448800-113455600	Weak transcription	GM12878-XiMat	blood
46	chr1:113448800-113458600	Weak transcription	Fetal Stomach	stomach
47	chr1:113448800-113459400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr1:113449000-113450200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:113449000-113450200	Weak transcription	HSMM	muscle
50	chr1:113449000-113452000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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