Variant report

Variant	rs12073750
Chromosome Location	chr1:113147169-113147170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:113144240..113147645-chr1:113160783..113163246,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000007341	Chromatin interaction
ENSG00000116489	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10399919	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102490	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes]
rs11102493	1.00[MEX][hapmap]
rs11102500	0.93[AFR][1000 genomes]
rs11102519	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11102521	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1175632	1.00[MEX][hapmap]
rs1175640	1.00[MEX][hapmap]
rs1175642	1.00[MEX][hapmap]
rs12060267	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12069022	1.00[ASW][hapmap];0.91[LWK][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs12069740	1.00[ASW][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12074157	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12077330	0.89[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12080006	0.93[AFR][1000 genomes]
rs12082350	0.86[AFR][1000 genomes]
rs12085734	1.00[MEX][hapmap]
rs12087862	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12091635	0.93[AFR][1000 genomes]
rs12094504	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs12095563	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17030350	1.00[MEX][hapmap]
rs17030446	1.00[ASW][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.86[AFR][1000 genomes]
rs17030451	0.82[YRI][hapmap];0.86[AFR][1000 genomes]
rs17030455	0.82[YRI][hapmap];0.88[AFR][1000 genomes]
rs17030475	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[YRI][hapmap];0.93[AFR][1000 genomes]
rs17030592	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4424506	1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs57573777	1.00[AMR][1000 genomes]
rs58634778	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59053530	1.00[AMR][1000 genomes]
rs59324334	0.88[AFR][1000 genomes]
rs61203550	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72982599	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984503	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72984509	1.00[AMR][1000 genomes]
rs72984515	1.00[AMR][1000 genomes]
rs72986505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72986535	1.00[AMR][1000 genomes]
rs72993070	0.82[AFR][1000 genomes]
rs72993072	0.93[AFR][1000 genomes]
rs7542272	1.00[MEX][hapmap]
rs9919308	0.84[ASW][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][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	esv13370	chr1:112693290-113246263	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
4	nsv432631	chr1:113071834-113200797	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	71 gene(s)	inside rSNPs	diseases
5	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	158 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113092000-113151200	Weak transcription	Colonic Mucosa	Colon
2	chr1:113109000-113160000	Weak transcription	Gastric	stomach
3	chr1:113109200-113152600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:113115400-113154200	Weak transcription	Esophagus	oesophagus
5	chr1:113115800-113160000	Weak transcription	Small Intestine	intestine
6	chr1:113116400-113160000	Weak transcription	Spleen	Spleen
7	chr1:113118000-113160800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr1:113118800-113160400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:113121000-113148400	Weak transcription	Stomach Mucosa	stomach
10	chr1:113124600-113148400	Weak transcription	NHLF	lung
11	chr1:113128000-113148400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr1:113129000-113147200	Strong transcription	HSMM	muscle
13	chr1:113129600-113159000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr1:113131400-113160000	Weak transcription	Fetal Heart	heart
15	chr1:113131600-113147200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:113132600-113148400	Weak transcription	Lung	lung
17	chr1:113132600-113148400	Weak transcription	Pancreas	Pancrea
18	chr1:113132600-113148400	Weak transcription	Thymus	Thymus
19	chr1:113132600-113152400	Weak transcription	Psoas Muscle	Psoas
20	chr1:113132600-113154800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr1:113132600-113159800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr1:113133000-113148400	Weak transcription	H1 Cell Line	embryonic stem cell
23	chr1:113133000-113148400	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:113133000-113148600	Weak transcription	HSMMtube	muscle
25	chr1:113133000-113152000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr1:113133000-113152400	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr1:113133000-113160000	Weak transcription	Fetal Brain Male	brain
28	chr1:113133000-113160800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr1:113133200-113148400	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr1:113133200-113148400	Weak transcription	GM12878-XiMat	blood
31	chr1:113133200-113148600	Weak transcription	A549	lung
32	chr1:113133200-113149800	Weak transcription	Primary B cells from peripheral blood	blood
33	chr1:113133200-113150800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr1:113133200-113159600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:113133200-113159600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
36	chr1:113133600-113148400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:113135400-113159800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr1:113136000-113147400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr1:113136200-113147400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:113136200-113156800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr1:113136600-113158800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr1:113136800-113159400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:113137000-113154200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr1:113137600-113160200	Weak transcription	Pancreatic Islets	Pancreatic Islet
45	chr1:113138000-113159400	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:113138400-113147400	Strong transcription	Liver	Liver
47	chr1:113139200-113159600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:113139600-113147400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr1:113139600-113148600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr1:113140000-113148400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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