Variant report

Variant	rs2462938
Chromosome Location	chr12:56128927-56128928
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56128209..56131175-chr12:56191287..56192790,2	MCF-7	breast:
2	chr12:56127900..56130507-chr12:56583314..56585009,2	K562	blood:
3	chr12:56128491..56132678-chr12:56134367..56139397,6	MCF-7	breast:
4	chr12:56126916..56129373-chr12:56137804..56139318,2	K562	blood:
5	chr12:56127218..56129412-chr12:56319218..56320927,2	K562	blood:

Variant related genes	Relation type
ENSG00000139613	Chromatin interaction
ENSG00000135414	Chromatin interaction
ENSG00000258199	Chromatin interaction
ENSG00000170473	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1466512	1.00[AMR][1000 genomes]
rs1681085	1.00[AMR][1000 genomes]
rs1725358	1.00[AMR][1000 genomes]
rs1871999	1.00[AMR][1000 genomes]
rs2449476	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2694008	1.00[AMR][1000 genomes]
rs2694015	1.00[AMR][1000 genomes]
rs2887997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4759012	1.00[AMR][1000 genomes]
rs4759202	1.00[AMR][1000 genomes]
rs55884432	1.00[AMR][1000 genomes]
rs6581083	1.00[AMR][1000 genomes]
rs7294345	1.00[AMR][1000 genomes]
rs7310325	1.00[AMR][1000 genomes]
rs772250	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772252	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs772256	1.00[AMR][1000 genomes]
rs772257	1.00[AMR][1000 genomes]
rs772259	1.00[AMR][1000 genomes]
rs772260	1.00[AMR][1000 genomes]
rs772261	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7956337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7963379	1.00[AMR][1000 genomes]
rs812230	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832423	chr12:56080822-56253698	Flanking Active TSS Strong transcription Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	119 gene(s)	inside rSNPs	diseases
2	nsv469410	chr12:56098038-56170893	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
3	nsv559004	chr12:56098038-56170893	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56124000-56130800	Weak transcription	Aorta	Aorta
2	chr12:56124000-56131200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr12:56124400-56130600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:56124400-56130600	Weak transcription	Placenta	Placenta
5	chr12:56124400-56130800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:56124400-56130800	Weak transcription	Left Ventricle	heart
7	chr12:56124400-56131000	Weak transcription	Colonic Mucosa	Colon
8	chr12:56124400-56131000	Weak transcription	Esophagus	oesophagus
9	chr12:56124400-56131600	Weak transcription	Gastric	stomach
10	chr12:56124600-56130400	Weak transcription	Fetal Intestine Large	intestine
11	chr12:56124600-56130600	Weak transcription	Right Atrium	heart
12	chr12:56124600-56130800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:56124600-56130800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr12:56124600-56130800	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:56124600-56130800	Weak transcription	K562	blood
16	chr12:56124600-56131000	Weak transcription	Primary B cells from cord blood	blood
17	chr12:56124600-56131000	Weak transcription	A549	lung
18	chr12:56124600-56131600	Weak transcription	Spleen	Spleen
19	chr12:56124600-56131800	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr12:56124600-56131800	Weak transcription	NHEK	skin
21	chr12:56124800-56129800	Weak transcription	Brain Germinal Matrix	brain
22	chr12:56124800-56129800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr12:56124800-56130000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:56124800-56130400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr12:56124800-56130600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr12:56124800-56130600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:56124800-56130600	Weak transcription	Primary hematopoietic stem cells	blood
28	chr12:56124800-56130600	Weak transcription	Brain Substantia Nigra	brain
29	chr12:56124800-56130600	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr12:56124800-56130800	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:56124800-56130800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr12:56124800-56130800	Weak transcription	Fetal Brain Female	brain
33	chr12:56124800-56130800	Weak transcription	Fetal Kidney	kidney
34	chr12:56124800-56130800	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr12:56124800-56130800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr12:56124800-56131000	Weak transcription	Thymus	Thymus
37	chr12:56124800-56131400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr12:56125000-56129800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:56125000-56130000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr12:56125000-56130200	Weak transcription	Fetal Heart	heart
41	chr12:56125000-56130600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:56125000-56130600	Weak transcription	Fetal Lung	lung
43	chr12:56125000-56130800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:56125000-56130800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr12:56125000-56130800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
46	chr12:56125000-56130800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr12:56125000-56131200	Weak transcription	Osteobl	bone
48	chr12:56125000-56132200	Weak transcription	Lung	lung
49	chr12:56125200-56130000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:56125200-56130800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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