Variant report

Variant	rs12040903
Chromosome Location	chr1:113254125-113254126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113160602..113163896-chr1:113252357..113259247,7	K562	blood:
2	chr1:113215712..113221627-chr1:113253708..113259381,5	MCF-7	breast:
3	chr1:113239573..113244483-chr1:113252369..113259292,10	K562	blood:
4	chr1:113166528..113169223-chr1:113253776..113256616,2	MCF-7	breast:
5	chr1:113253460..113256284-chr1:113256871..113259194,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000261595	Chromatin interaction
ENSG00000007341	Chromatin interaction
ENSG00000235299	Chromatin interaction
ENSG00000155367	Chromatin interaction
ENSG00000116489	Chromatin interaction
ENSG00000155363	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11102522	0.85[AMR][1000 genomes]
rs7522283	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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	esv18511	chr1:113246318-113350775	Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
9	nsv998794	chr1:113246630-113310418	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
10	nsv872157	chr1:113247467-113265819	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
11	nsv547566	chr1:113248365-113301657	Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
12	nsv872158	chr1:113250888-113265819	Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
13	nsv872159	chr1:113252091-113265819	Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Active TSS Enhancers Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113249000-113256400	Weak transcription	Fetal Heart	heart
2	chr1:113250400-113256000	Weak transcription	Brain Substantia Nigra	brain
3	chr1:113250400-113256000	Weak transcription	Right Ventricle	heart
4	chr1:113250400-113256200	Weak transcription	Esophagus	oesophagus
5	chr1:113250400-113256200	Weak transcription	Gastric	stomach
6	chr1:113250400-113256400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr1:113250400-113256600	Weak transcription	Brain Angular Gyrus	brain
8	chr1:113250400-113256600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr1:113250400-113256600	Weak transcription	Psoas Muscle	Psoas
10	chr1:113250400-113256800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr1:113250400-113256800	Weak transcription	Aorta	Aorta
12	chr1:113250600-113254200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:113250600-113255200	Weak transcription	Brain Hippocampus Middle	brain
14	chr1:113250600-113255800	Weak transcription	Liver	Liver
15	chr1:113250600-113256000	Weak transcription	Adipose Nuclei	Adipose
16	chr1:113250600-113256000	Weak transcription	Brain Anterior Caudate	brain
17	chr1:113250600-113256000	Weak transcription	Left Ventricle	heart
18	chr1:113250600-113256000	Weak transcription	Stomach Mucosa	stomach
19	chr1:113250600-113256200	Weak transcription	Pancreas	Pancrea
20	chr1:113250600-113256200	Weak transcription	Spleen	Spleen
21	chr1:113250600-113256600	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:113250600-113256800	Weak transcription	Colon Smooth Muscle	Colon
23	chr1:113250600-113257000	Weak transcription	HUVEC	blood vessel
24	chr1:113250800-113255600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr1:113250800-113256000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr1:113250800-113256200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr1:113250800-113256200	Weak transcription	Primary B cells from cord blood	blood
28	chr1:113250800-113256600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr1:113250800-113256600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr1:113250800-113256600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr1:113250800-113256600	Weak transcription	Osteobl	bone
32	chr1:113251000-113256200	Weak transcription	HMEC	breast
33	chr1:113251000-113256400	Weak transcription	NHEK	skin
34	chr1:113251000-113257200	Weak transcription	Hela-S3	cervix
35	chr1:113251400-113256200	Weak transcription	K562	blood
36	chr1:113251400-113256800	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr1:113252000-113255600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:113252400-113254400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
39	chr1:113252400-113255600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:113253000-113256000	Weak transcription	GM12878-XiMat	blood
41	chr1:113253400-113254200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr1:113253400-113254400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
43	chr1:113253400-113256000	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr1:113253400-113256200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr1:113253400-113256400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr1:113253600-113254200	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr1:113253800-113254400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:113253800-113254400	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr1:113253800-113254400	Bivalent Enhancer	Fetal Thymus	thymus
50	chr1:113253800-113254800	Enhancers	iPS-18 Cell Line	embryonic stem cell

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