Variant report

Variant	rs12649466
Chromosome Location	chr4:3390900-3390901
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3385272..3387718-chr4:3389014..3391654,3	MCF-7	breast:
2	chr4:3388642..3391528-chr4:3405332..3407484,2	MCF-7	breast:
3	chr4:3356602..3361196-chr4:3388835..3391854,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000159788	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11730455	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11732375	0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs12648723	0.96[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28409520	0.95[ASN][1000 genomes]
rs35563310	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6852186	1.00[JPT][hapmap];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer 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	12 gene(s)	inside rSNPs	diseases
6	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
7	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv878463	chr4:3363994-3498896	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv428435	chr4:3386773-3623321	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3386200-3391400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr4:3386400-3391200	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr4:3386600-3392400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr4:3386600-3393800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:3386800-3393600	Enhancers	H1 Cell Line	embryonic stem cell
6	chr4:3386800-3393600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr4:3386800-3395800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr4:3387600-3392600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr4:3387800-3391000	Active TSS	Esophagus	oesophagus
10	chr4:3388000-3394400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:3388400-3391200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr4:3388400-3392000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr4:3388400-3393600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
14	chr4:3388600-3392000	Enhancers	ES-I3 Cell Line	embryonic stem cell
15	chr4:3388600-3392400	Enhancers	Fetal Muscle Trunk	muscle
16	chr4:3388600-3394400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr4:3388800-3391200	Enhancers	Fetal Intestine Small	intestine
18	chr4:3388800-3391400	Enhancers	Fetal Heart	heart
19	chr4:3388800-3391600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr4:3388800-3391800	Enhancers	Fetal Muscle Leg	muscle
21	chr4:3388800-3392000	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr4:3388800-3392600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr4:3388800-3392600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
24	chr4:3388800-3392800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr4:3388800-3394400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr4:3389000-3391600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr4:3389000-3391800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:3389000-3393400	Enhancers	Brain Germinal Matrix	brain
29	chr4:3389200-3391000	Active TSS	Duodenum Mucosa	Duodenum
30	chr4:3389200-3391200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr4:3389200-3391200	Active TSS	Rectal Mucosa Donor 31	rectum
32	chr4:3389200-3391400	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr4:3389200-3391400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
34	chr4:3389200-3391400	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr4:3389200-3395000	Weak transcription	HepG2	liver
36	chr4:3389200-3403400	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr4:3389400-3391000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr4:3389400-3391000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr4:3389400-3391000	Weak transcription	Spleen	Spleen
40	chr4:3389400-3391000	Active TSS	NHDF-Ad	bronchial
41	chr4:3389400-3391600	Flanking Active TSS	Osteobl	bone
42	chr4:3389600-3391000	Enhancers	Fetal Brain Female	brain
43	chr4:3389600-3391200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr4:3389600-3391200	Bivalent Enhancer	Fetal Thymus	thymus
45	chr4:3389600-3391400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
46	chr4:3389600-3391400	Flanking Active TSS	Stomach Smooth Muscle	stomach
47	chr4:3389600-3391600	Active TSS	Rectal Smooth Muscle	rectum
48	chr4:3389800-3391000	Enhancers	Primary T cells from cord blood	blood
49	chr4:3389800-3391000	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr4:3389800-3391000	Active TSS	Colonic Mucosa	Colon

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