Variant report

Variant	rs1273952
Chromosome Location	chr12:56300748-56300749
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:56299195..56301472-chr12:56319944..56322489,2	MCF-7	breast:
2	chr12:56299851..56302754-chr12:56309766..56311524,2	K562	blood:
3	chr12:56300343..56307033-chr12:56318864..56323986,11	MCF-7	breast:

Variant related genes	Relation type
ENSG00000065357	Chromatin interaction
ENSG00000170473	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs1681078	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1689509	0.82[LWK][hapmap];1.00[MEX][hapmap]
rs2069400	0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs2640568	0.82[LWK][hapmap];1.00[MEX][hapmap]
rs705697	0.82[LWK][hapmap];1.00[MEX][hapmap]
rs7302270	0.87[LWK][hapmap];1.00[MEX][hapmap]
rs772464	0.82[LWK][hapmap];1.00[MEX][hapmap]
rs772466	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051961	chr12:56262220-56629427	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	284 gene(s)	inside rSNPs	diseases
2	nsv832424	chr12:56275226-56466917	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56279800-56320000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:56285200-56320000	Weak transcription	Pancreas	Pancrea
3	chr12:56291000-56308400	Weak transcription	Right Atrium	heart
4	chr12:56291400-56319000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr12:56292800-56316000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr12:56293000-56307800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
7	chr12:56293200-56307000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr12:56293200-56307200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:56293200-56307400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr12:56293600-56319200	Weak transcription	Primary hematopoietic stem cells	blood
11	chr12:56293800-56319600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr12:56294200-56302600	Weak transcription	Brain Anterior Caudate	brain
13	chr12:56294200-56319400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr12:56294400-56302800	Weak transcription	Stomach Mucosa	stomach
15	chr12:56294400-56313800	Weak transcription	Ovary	ovary
16	chr12:56294400-56319600	Weak transcription	Colon Smooth Muscle	Colon
17	chr12:56294600-56308000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr12:56296000-56301400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr12:56296000-56307800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr12:56296000-56319600	Weak transcription	Right Ventricle	heart
21	chr12:56296200-56303000	Weak transcription	Small Intestine	intestine
22	chr12:56296200-56319400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:56296400-56302600	Weak transcription	K562	blood
24	chr12:56296800-56306800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr12:56296800-56319600	Weak transcription	Placenta Amnion	Placenta Amnion
26	chr12:56297000-56315800	Weak transcription	Aorta	Aorta
27	chr12:56297200-56301800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:56297200-56302800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:56297200-56305400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr12:56297200-56306200	Weak transcription	Placenta	Placenta
31	chr12:56297200-56306800	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr12:56297200-56306800	Weak transcription	Primary T cells from cord blood	blood
33	chr12:56297200-56306800	Weak transcription	HSMM	muscle
34	chr12:56297200-56307600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
35	chr12:56297200-56315600	Weak transcription	Fetal Brain Female	brain
36	chr12:56297200-56315600	Weak transcription	Lung	lung
37	chr12:56297200-56315800	Weak transcription	H9 Cell Line	embryonic stem cell
38	chr12:56297200-56319200	Weak transcription	Colonic Mucosa	Colon
39	chr12:56297200-56319600	Weak transcription	Brain Germinal Matrix	brain
40	chr12:56297200-56319600	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr12:56297200-56320000	Weak transcription	Gastric	stomach
42	chr12:56297200-56320000	Weak transcription	Spleen	Spleen
43	chr12:56297400-56302600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr12:56297400-56302600	Weak transcription	Brain Hippocampus Middle	brain
45	chr12:56297400-56302600	Weak transcription	Brain Substantia Nigra	brain
46	chr12:56297400-56302600	Weak transcription	Fetal Intestine Small	intestine
47	chr12:56297400-56302600	Weak transcription	HepG2	liver
48	chr12:56297400-56305200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr12:56297400-56306000	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr12:56297400-56306200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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