Variant report

Variant	rs1793923
Chromosome Location	chr12:48384122-48384123
allele	A/G
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	MEF2A	chr12:48384007-48384451	GM12878	blood:	n/a	chr12:48384209-48384217
2	ETS1	chr12:48384031-48384355	GM12878	blood:	n/a	n/a
3	SPI1	chr12:48383971-48384436	GM12891	blood:	n/a	chr12:48384344-48384351 chr12:48384210-48384219
4	BCLAF1	chr12:48383996-48384506	GM12878	blood:	n/a	chr12:48384210-48384219
5	MAX	chr12:48384038-48384502	NB4	blood:	n/a	chr12:48384230-48384240
6	NFIC	chr12:48384026-48384445	GM12878	blood:	n/a	n/a
7	MTA3	chr12:48384030-48384581	GM12878	blood:	n/a	n/a
8	SPI1	chr12:48383998-48384477	GM12891	blood:	n/a	chr12:48384344-48384351 chr12:48384210-48384219
9	MYC	chr12:48384068-48384491	NB4	blood:	n/a	chr12:48384230-48384240
10	SPI1	chr12:48384032-48384531	HL-60	blood:	n/a	chr12:48384344-48384351 chr12:48384210-48384219
11	SPI1	chr12:48384040-48384344	GM12878	blood:	n/a	chr12:48384210-48384219
12	RUNX3	chr12:48383978-48384671	GM12878	blood:	n/a	n/a
13	SPI1	chr12:48383870-48384649	GM12878	blood:	n/a	chr12:48384344-48384351 chr12:48384210-48384219
14	SPI1	chr12:48383966-48384431	GM12878	blood:	n/a	chr12:48384344-48384351 chr12:48384210-48384219
15	RUNX3	chr12:48383965-48384549	GM12878	blood:	n/a	n/a
16	ELF1	chr12:48384114-48384435	GM12878	blood:	n/a	n/a
17	NFIC	chr12:48383977-48384450	GM12878	blood:	n/a	n/a

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: 25 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11168337	0.83[CHD][hapmap];0.98[TSI][hapmap];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	1.00[JPT][hapmap];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	0.82[CEU][hapmap];0.87[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.83[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];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]
rs1635550	0.81[JPT][hapmap]
rs1635553	0.91[TSI][hapmap];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]
rs1793924	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2276454	0.80[GIH][hapmap];0.83[TSI][hapmap]
rs3829734	0.81[ASN][1000 genomes]
rs3829736	0.87[EUR][1000 genomes]
rs740024	1.00[ASW][hapmap];0.92[CEU][hapmap];0.87[CHB][hapmap];0.98[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.95[LWK][hapmap];0.87[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs917055	0.82[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs1793923	PRPF40B	cis	parietal	SCAN
rs1793923	C12orf68	cis	parietal	SCAN
rs1793923	LMBR1L	cis	cerebellum	SCAN
rs1793923	PRKAG1	cis	parietal	SCAN
rs1793923	SNORA2A	cis	parietal	SCAN
rs1793923	PRICKLE1	cis	parietal	SCAN
rs1793923	PROCA1	trans	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48376800-48391000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:48381200-48385400	Enhancers	Fetal Muscle Leg	muscle
3	chr12:48381200-48385800	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr12:48381400-48384400	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:48381400-48386400	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:48381400-48386800	Genic enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:48381400-48388800	Weak transcription	Fetal Intestine Small	intestine
8	chr12:48382200-48385000	Weak transcription	Right Atrium	heart
9	chr12:48382600-48384400	Weak transcription	Fetal Brain Male	brain
10	chr12:48382600-48384400	Weak transcription	Fetal Brain Female	brain
11	chr12:48382800-48384800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr12:48382800-48385200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
13	chr12:48382800-48385800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
14	chr12:48382800-48394600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr12:48383000-48385000	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:48383000-48385200	Weak transcription	Brain Germinal Matrix	brain
17	chr12:48383000-48385200	Enhancers	Fetal Thymus	thymus
18	chr12:48383000-48385400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr12:48383000-48385600	Enhancers	Spleen	Spleen
20	chr12:48383000-48388400	Weak transcription	Psoas Muscle	Psoas
21	chr12:48383200-48384200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr12:48383200-48384800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr12:48383200-48385000	Enhancers	Primary T cells from cord blood	blood
24	chr12:48383200-48385000	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr12:48383200-48385200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr12:48383200-48385200	Enhancers	Primary T helper naive cells from peripheral blood	blood
27	chr12:48383200-48385400	Enhancers	Primary B cells from cord blood	blood
28	chr12:48383200-48385400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:48383200-48385600	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr12:48383200-48385600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
31	chr12:48383200-48385600	Enhancers	Dnd41	blood
32	chr12:48383400-48384800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr12:48383400-48385000	Enhancers	Primary hematopoietic stem cells	blood
34	chr12:48383400-48385200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr12:48383400-48385200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr12:48383400-48385200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
37	chr12:48383400-48385200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
38	chr12:48383400-48385200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr12:48383400-48385400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:48383600-48384800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr12:48383600-48384800	Bivalent Enhancer	Thymus	Thymus
42	chr12:48383800-48384600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr12:48383800-48384600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
44	chr12:48383800-48385000	Weak transcription	Lung	lung
45	chr12:48383800-48385000	Enhancers	Skeletal Muscle Male	skeletal muscle
46	chr12:48383800-48393800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr12:48383800-48394400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:48384000-48384200	Flanking Active TSS	GM12878-XiMat	blood
49	chr12:48384000-48386000	Bivalent Enhancer	Fetal Muscle Trunk	muscle

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