Variant report

Variant	rs12470881
Chromosome Location	chr2:10144404-10144405
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:10141557..10144433-chr2:10145259..10147096,2	MCF-7	breast:
2	chr2:10143972..10145495-chr2:10148319..10150993,2	K562	blood:
3	chr2:10141011..10144036-chr2:10144143..10145916,3	K562	blood:

Variant related genes	Relation type
ENSG00000188525	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11246	0.82[JPT][hapmap]
rs12477748	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12618788	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[YRI][hapmap]
rs12623004	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs1367383	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs1367388	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs1367389	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs1465638	0.82[JPT][hapmap]
rs1549753	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs1549754	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs2011516	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs2303920	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs34521538	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3791753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs3791760	0.81[JPT][hapmap]
rs3828260	0.87[CHB][hapmap]
rs4669511	0.87[CHB][hapmap]
rs4669517	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6432047	0.93[CHB][hapmap];0.88[JPT][hapmap]
rs731453	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs891500	0.93[CHB][hapmap];0.87[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011125	chr2:9996740-10293803	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
2	nsv1011689	chr2:10023891-10293803	Flanking Active TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv1002769	chr2:10064511-10157028	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv997334	chr2:10080327-10189279	Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS 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	32 gene(s)	inside rSNPs	diseases
5	nsv828297	chr2:10109299-10236332	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10101400-10144800	Weak transcription	Brain Germinal Matrix	brain
2	chr2:10115000-10148000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr2:10124800-10149400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:10125000-10147600	Weak transcription	K562	blood
5	chr2:10125000-10149400	Weak transcription	Psoas Muscle	Psoas
6	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:10128000-10146400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:10131600-10149600	Weak transcription	Brain Substantia Nigra	brain
9	chr2:10132200-10145200	Weak transcription	Fetal Intestine Large	intestine
10	chr2:10132200-10146800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr2:10132400-10146400	Weak transcription	Left Ventricle	heart
12	chr2:10132400-10146800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr2:10133200-10146400	Weak transcription	Colon Smooth Muscle	Colon
14	chr2:10134000-10145600	Weak transcription	Fetal Kidney	kidney
15	chr2:10134000-10145800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:10134200-10147000	Weak transcription	HSMMtube	muscle
17	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:10135400-10146400	Weak transcription	HUVEC	blood vessel
19	chr2:10136000-10144600	Weak transcription	Spleen	Spleen
20	chr2:10137000-10148000	Weak transcription	Hela-S3	cervix
21	chr2:10137200-10144600	Weak transcription	Brain Angular Gyrus	brain
22	chr2:10137200-10146200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:10137600-10146400	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr2:10137600-10146600	Weak transcription	Fetal Heart	heart
25	chr2:10137600-10146800	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr2:10137600-10149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
27	chr2:10137800-10146400	Weak transcription	Fetal Brain Female	brain
28	chr2:10139600-10147000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr2:10139800-10146400	Weak transcription	Gastric	stomach
30	chr2:10139800-10150400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr2:10141000-10144600	Weak transcription	Fetal Muscle Leg	muscle
32	chr2:10141000-10147000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:10141400-10145200	Weak transcription	Fetal Intestine Small	intestine
34	chr2:10141400-10146400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:10141400-10146800	Weak transcription	Lung	lung
36	chr2:10141600-10160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr2:10142000-10144800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr2:10142000-10146400	Weak transcription	Liver	Liver
39	chr2:10142000-10147600	Weak transcription	HepG2	liver
40	chr2:10142400-10148200	Enhancers	Adipose Nuclei	Adipose
41	chr2:10142600-10147000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr2:10142800-10145800	Enhancers	NHDF-Ad	bronchial
43	chr2:10142800-10148000	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr2:10143800-10145800	Weak transcription	Pancreas	Pancrea
45	chr2:10143800-10147200	Weak transcription	Osteobl	bone
46	chr2:10144000-10145200	Enhancers	Placenta Amnion	Placenta Amnion
47	chr2:10144200-10144800	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr2:10144200-10144800	Enhancers	Stomach Smooth Muscle	stomach
49	chr2:10144200-10145200	Enhancers	Placenta	Placenta
50	chr2:10144200-10146800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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