Variant report

Variant	rs12468647
Chromosome Location	chr2:10149956-10149957
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	RFX5	chr2:10148813-10150803	SK-N-SH	brain:	n/a	n/a
2	RXRA	chr2:10149948-10150629	HepG2	liver:	n/a	chr2:10150273-10150287
3	RFX5	chr2:10149946-10150668	IMR90	lung:	n/a	n/a
4	EP300	chr2:10148723-10151084	SK-N-SH	brain:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:10148500..10150133-chr2:10169876..10172659,2	K562	blood:
2	chr2:10148714..10150676-chr2:10152229..10153770,2	MCF-7	breast:
3	chr2:10147491..10150465-chr2:10152525..10155691,3	MCF-7	breast:
4	chr2:10143972..10145495-chr2:10148319..10150993,2	K562	blood:
5	chr2:10149097..10150727-chr2:10180461..10182958,2	MCF-7	breast:
6	chr2:10147901..10149984-chr2:10215589..10217531,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CYS1-3	chr2:10149520-10149991	XLOC_001983

No data

Variant related genes	Relation type
ENSG00000188525	TF binding region
ENSG00000260077	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12992130	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12998233	0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4669518	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6713766	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]

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:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:10125200-10150000	Weak transcription	Brain Hippocampus Middle	brain
2	chr2:10134800-10150600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:10139800-10150400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:10141600-10160200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:10145800-10151000	Enhancers	Pancreas	Pancrea
6	chr2:10146400-10150800	Enhancers	Colon Smooth Muscle	Colon
7	chr2:10146400-10150800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr2:10146400-10151200	Enhancers	Placenta	Placenta
9	chr2:10146800-10150200	Enhancers	Rectal Smooth Muscle	rectum
10	chr2:10146800-10150800	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr2:10146800-10150800	Enhancers	HSMM	muscle
12	chr2:10146800-10151000	Enhancers	NHDF-Ad	bronchial
13	chr2:10146800-10151200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:10147000-10150600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr2:10147000-10150800	Enhancers	HSMMtube	muscle
16	chr2:10147200-10150600	Weak transcription	Esophagus	oesophagus
17	chr2:10147200-10150800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr2:10147200-10151200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr2:10147600-10151000	Enhancers	NHLF	lung
20	chr2:10147800-10151200	Enhancers	Fetal Muscle Leg	muscle
21	chr2:10148200-10151000	Enhancers	Ovary	ovary
22	chr2:10148200-10151800	Enhancers	Lung	lung
23	chr2:10148400-10150200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:10148400-10151200	Enhancers	Right Ventricle	heart
25	chr2:10148600-10150000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:10148800-10153000	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr2:10149000-10150800	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr2:10149000-10150800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:10149200-10150200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
30	chr2:10149200-10150400	Enhancers	Liver	Liver
31	chr2:10149200-10150600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr2:10149200-10151000	Enhancers	Colonic Mucosa	Colon
33	chr2:10149200-10151000	Enhancers	Left Ventricle	heart
34	chr2:10149200-10151000	Enhancers	Right Atrium	heart
35	chr2:10149200-10151000	Enhancers	Osteobl	bone
36	chr2:10149200-10151600	Enhancers	Spleen	Spleen
37	chr2:10149200-10152000	Enhancers	Gastric	stomach
38	chr2:10149400-10150000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr2:10149400-10150400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:10149400-10150800	Enhancers	Brain Anterior Caudate	brain
41	chr2:10149400-10150800	Bivalent Enhancer	Fetal Stomach	stomach
42	chr2:10149400-10150800	Enhancers	Psoas Muscle	Psoas
43	chr2:10149400-10151200	Enhancers	Duodenum Mucosa	Duodenum
44	chr2:10149600-10150000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:10149600-10150400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
46	chr2:10149600-10150600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr2:10149600-10150600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:10149600-10150800	Enhancers	Sigmoid Colon	Sigmoid Colon
49	chr2:10149600-10150800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
50	chr2:10149600-10151000	Enhancers	Stomach Mucosa	stomach

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