Variant report

Variant	rs1238407
Chromosome Location	chr12:45661843-45661844
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:45608867..45611459-chr12:45661103..45665633,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134297	Chromatin interaction
ENSG00000177119	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1004598	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1019584	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10748414	0.80[AFR][1000 genomes]
rs10748417	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10748418	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10748420	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10785559	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs10785565	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10785568	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs10880767	0.90[AMR][1000 genomes]
rs10880773	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11182971	0.90[AMR][1000 genomes]
rs1862907	0.90[AMR][1000 genomes]
rs1877972	0.90[AMR][1000 genomes]
rs1896027	0.83[AFR][1000 genomes]
rs1913691	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2037855	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4140756	1.00[AMR][1000 genomes]
rs4768087	0.83[AFR][1000 genomes]
rs4768604	0.90[AMR][1000 genomes]
rs6582542	0.89[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6582543	0.90[AMR][1000 genomes]
rs7135029	0.83[AFR][1000 genomes]
rs7953360	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7960422	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7970250	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7970619	0.90[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050923	chr12:45581310-45808289	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:45636200-45662400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr12:45651200-45662000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr12:45651400-45662000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr12:45651400-45662400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr12:45651400-45675600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:45651600-45662000	Weak transcription	Fetal Muscle Leg	muscle
7	chr12:45651600-45662400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:45651600-45667000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:45651600-45667400	Weak transcription	Brain Substantia Nigra	brain
10	chr12:45651600-45674000	Weak transcription	Primary B cells from cord blood	blood
11	chr12:45653800-45662000	Weak transcription	Esophagus	oesophagus
12	chr12:45654200-45662000	Weak transcription	Right Ventricle	heart
13	chr12:45654200-45662000	Weak transcription	Spleen	Spleen
14	chr12:45654200-45662400	Weak transcription	Gastric	stomach
15	chr12:45654200-45666800	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr12:45654400-45662000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr12:45654400-45662000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:45654400-45662000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
19	chr12:45654400-45662000	Weak transcription	Osteobl	bone
20	chr12:45654400-45662400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr12:45654400-45662400	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr12:45654400-45662400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr12:45654400-45662400	Weak transcription	Fetal Stomach	stomach
24	chr12:45654400-45662400	Weak transcription	HSMM	muscle
25	chr12:45654400-45662400	Weak transcription	NH-A	brain
26	chr12:45654400-45662400	Weak transcription	NHLF	lung
27	chr12:45654400-45662600	Weak transcription	Stomach Mucosa	stomach
28	chr12:45654400-45666600	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr12:45654400-45667600	Weak transcription	Primary T cells from cord blood	blood
30	chr12:45654400-45725600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:45654800-45662000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr12:45655000-45662000	Weak transcription	Lung	lung
33	chr12:45656000-45662000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:45656800-45662400	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr12:45657200-45662000	Weak transcription	Thymus	Thymus
36	chr12:45657600-45662000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr12:45657600-45662000	Weak transcription	Psoas Muscle	Psoas
38	chr12:45657800-45662000	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr12:45657800-45662200	Weak transcription	Duodenum Mucosa	Duodenum
40	chr12:45658000-45662000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr12:45658000-45662000	Weak transcription	Fetal Thymus	thymus
42	chr12:45658000-45662600	Weak transcription	HepG2	liver
43	chr12:45658200-45662000	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr12:45658200-45662400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr12:45658200-45662400	Weak transcription	Liver	Liver
46	chr12:45658200-45662400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr12:45658200-45662400	Weak transcription	GM12878-XiMat	blood
48	chr12:45658200-45662400	Weak transcription	K562	blood
49	chr12:45658600-45662400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr12:45658800-45662000	Weak transcription	Small Intestine	intestine

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