Variant report

Variant	rs1793924
Chromosome Location	chr12:48383953-48383954
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr12:48383870-48384649	GM12878	blood:	n/a	chr12:48384344-48384351 chr12:48384210-48384219

No.	Distal block	Cell Line	Cell type
1	chr12:48373823..48376376-chr12:48383731..48387007,3	MCF-7	breast:
2	chr12:48382599..48384881-chr12:48386422..48387977,2	MCF-7	breast:
3	chr12:48383628..48385806-chr12:48436712..48438837,2	K562	blood:

Variant related genes	Relation type
COL2A1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11168337	0.87[EUR][1000 genomes]
rs1621710	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1635534	0.96[ASN][1000 genomes]
rs1635535	0.96[ASN][1000 genomes]
rs1635536	0.92[ASN][1000 genomes]
rs1635537	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1635544	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1635546	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1635547	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1635553	0.82[EUR][1000 genomes]
rs1793911	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1793912	0.96[ASN][1000 genomes]
rs1793913	0.96[ASN][1000 genomes]
rs1793915	0.95[ASN][1000 genomes]
rs1793917	0.92[ASN][1000 genomes]
rs1793923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3829734	0.81[ASN][1000 genomes]
rs3829736	0.87[EUR][1000 genomes]
rs740024	0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917055	0.92[ASN][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	nsv832401	chr12:48347453-48477999	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv899061	chr12:48360620-48389023	Bivalent Enhancer Enhancers Strong transcription Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv519659	chr12:48366449-48389245	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48359200-48384000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
3	chr12:48381200-48385400	Enhancers	Fetal Muscle Leg	muscle
4	chr12:48381200-48385800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr12:48381400-48384400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
7	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
9	chr12:48382200-48385000	Weak transcription	Right Atrium	heart
10	chr12:48382600-48384400	Weak transcription	Fetal Brain Male	brain
11	chr12:48382600-48384400	Weak transcription	Fetal Brain Female	brain
12	chr12:48382800-48384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:48382800-48385200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:48382800-48385800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr12:48383000-48385000	Weak transcription	Skeletal Muscle Female	skeletal muscle
17	chr12:48383000-48385200	Weak transcription	Brain Germinal Matrix	brain
18	chr12:48383000-48385200	Enhancers	Fetal Thymus	thymus
19	chr12:48383000-48385400	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr12:48383000-48385600	Enhancers	Spleen	Spleen
21	chr12:48383000-48388400	Weak transcription	Psoas Muscle	Psoas
22	chr12:48383200-48384000	Enhancers	GM12878-XiMat	blood
23	chr12:48383200-48384200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr12:48383200-48384800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:48383200-48385000	Enhancers	Primary T cells from cord blood	blood
26	chr12:48383200-48385000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr12:48383200-48385200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:48383200-48385200	Enhancers	Primary T helper naive cells from peripheral blood	blood
29	chr12:48383200-48385400	Enhancers	Primary B cells from cord blood	blood
30	chr12:48383200-48385400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:48383200-48385600	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr12:48383200-48385600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
33	chr12:48383200-48385600	Enhancers	Dnd41	blood
34	chr12:48383400-48384800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:48383400-48385000	Enhancers	Primary hematopoietic stem cells	blood
36	chr12:48383400-48385200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr12:48383400-48385200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
38	chr12:48383400-48385200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
39	chr12:48383400-48385200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr12:48383400-48385200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:48383400-48385400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr12:48383600-48384800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:48383600-48384800	Bivalent Enhancer	Thymus	Thymus
44	chr12:48383800-48384600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
45	chr12:48383800-48384600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr12:48383800-48385000	Weak transcription	Lung	lung
47	chr12:48383800-48385000	Enhancers	Skeletal Muscle Male	skeletal muscle
48	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
49	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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