Variant report

Variant	rs11574038
Chromosome Location	chr12:48277153-48277154
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	POLR2A	chr12:48276790-48277307	GM12892	blood:	n/a	n/a
2	TBL1XR1	chr12:48276856-48277451	GM12878	blood:	n/a	n/a
3	POLR2A	chr12:48276878-48277187	GM12878	blood:	n/a	n/a
4	NFATC1	chr12:48276894-48277481	GM12878	blood:	n/a	n/a
5	BHLHE40	chr12:48276970-48277403	GM12878	blood:	n/a	n/a
6	RELA	chr12:48276749-48277428	GM19099	blood:	n/a	n/a
7	IKZF1	chr12:48276608-48277471	GM12878	blood:	n/a	n/a
8	TCF12	chr12:48276948-48277456	GM12878	blood:	n/a	chr12:48277297-48277304
9	FOXM1	chr12:48276725-48277599	GM12878	blood:	n/a	n/a
10	POLR2A	chr12:48276650-48277565	GM12878	blood:	n/a	n/a
11	MAZ	chr12:48276901-48277498	GM12878	blood:	n/a	n/a
12	PAX5	chr12:48276426-48277515	GM12878	blood:	n/a	chr12:48277344-48277353 chr12:48277028-48277037 chr12:48277457-48277466
13	CEBPB	chr12:48276990-48277304	GM12878	blood:	n/a	n/a
14	ELF1	chr12:48276888-48277395	GM12878	blood:	n/a	n/a
15	YY1	chr12:48276919-48277315	GM12878	blood:	n/a	chr12:48277007-48277018 chr12:48276973-48276992
16	EBF1	chr12:48276500-48277592	GM12878	blood:	n/a	chr12:48277088-48277099
17	MAX	chr12:48276828-48277399	GM12878	blood:	n/a	n/a
18	BCLAF1	chr12:48276822-48277564	GM12878	blood:	n/a	chr12:48277009-48277022 chr12:48277344-48277353
19	RCOR1	chr12:48276596-48277379	GM12878	blood:	n/a	n/a
20	EP300	chr12:48276979-48277357	GM12878	blood:	n/a	chr12:48277009-48277025
21	ELF1	chr12:48276498-48277386	GM12878	blood:	n/a	n/a
22	ZNF143	chr12:48276992-48277394	GM12878	blood:	n/a	n/a
23	ATF2	chr12:48276893-48277405	GM12878	blood:	n/a	n/a
24	BCL11A	chr12:48276899-48277450	GM12878	blood:	n/a	chr12:48277009-48277022 chr12:48277344-48277353
25	ATF2	chr12:48276719-48277476	GM12878	blood:	n/a	n/a
26	TAF1	chr12:48276972-48277351	GM12878	blood:	n/a	n/a
27	TCF3	chr12:48276948-48277392	GM12878	blood:	n/a	chr12:48277153-48277168 chr12:48277156-48277165 chr12:48277108-48277122 chr12:48277154-48277168
28	EBF1	chr12:48276879-48277374	GM12878	blood:	n/a	chr12:48277088-48277099
29	PAX5	chr12:48276991-48277259	GM12878	blood:	n/a	chr12:48277028-48277037
30	MXI1	chr12:48276901-48277397	GM12878	blood:	n/a	n/a
31	ZEB1	chr12:48276854-48277343	GM12878	blood:	n/a	n/a
32	IRF4	chr12:48276769-48277390	GM12878	blood:	n/a	n/a
33	YY1	chr12:48277028-48277367	GM12892	blood:	n/a	n/a
34	MEF2A	chr12:48276867-48277482	GM12878	blood:	n/a	n/a
35	CHD2	chr12:48276550-48277408	GM12878	blood:	n/a	n/a
36	POLR2A	chr12:48276526-48277614	GM12892	blood:	n/a	n/a
37	EP300	chr12:48276921-48277403	GM12878	blood:	n/a	chr12:48277009-48277025
38	PML	chr12:48276708-48277693	GM12878	blood:	n/a	n/a
39	MEF2C	chr12:48276846-48277536	GM12878	blood:	n/a	n/a
40	IRF4	chr12:48276834-48277322	GM12878	blood:	n/a	n/a
41	BCL3	chr12:48276904-48277302	GM12878	blood:	n/a	chr12:48277009-48277022
42	NFIC	chr12:48276434-48277489	GM12878	blood:	n/a	n/a
43	FOXM1	chr12:48276703-48277512	GM12878	blood:	n/a	n/a
44	SP1	chr12:48276911-48277420	GM12878	blood:	n/a	n/a
45	POLR2A	chr12:48276915-48277553	GM12892	blood:	n/a	n/a
46	MAX	chr12:48276646-48277209	H1-hESC	embryonic stem cell:	n/a	n/a
47	TCF3	chr12:48276653-48277518	GM12878	blood:	n/a	chr12:48277153-48277168 chr12:48277156-48277165 chr12:48277108-48277122 chr12:48277154-48277168
48	MAX	chr12:48276779-48277203	H1-hESC	embryonic stem cell:	n/a	n/a
49	CEBPB	chr12:48276861-48277586	GM12878	blood:	n/a	n/a
50	E2F6	chr12:48276585-48277240	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:48276795..48279456-chr12:48285534..48287746,2	MCF-7	breast:
2	chr12:48276825..48278640-chr12:48287655..48289892,3	MCF-7	breast:
3	chr12:48276120..48279378-chr12:48295337..48299363,4	MCF-7	breast:

Variant related genes	Relation type
VDR	TF binding region
ENSG00000111424	Chromatin interaction

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs11168312	1.00[MEX][hapmap]
rs61558228	0.82[AFR][1000 genomes]
rs7308119	1.00[CEU][hapmap]

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	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
2	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11574038	SYCE1	trans	lymphoblastoid	seeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48262000-48296800	Weak transcription	Aorta	Aorta
2	chr12:48265000-48283200	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr12:48273600-48277200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:48273800-48278800	Enhancers	NHDF-Ad	bronchial
5	chr12:48275000-48277200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr12:48275000-48277400	Enhancers	HSMM	muscle
7	chr12:48275000-48279800	Enhancers	Fetal Intestine Large	intestine
8	chr12:48275200-48277600	Enhancers	Hela-S3	cervix
9	chr12:48275200-48278000	Enhancers	NH-A	brain
10	chr12:48275200-48279200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr12:48275200-48280000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:48275200-48280200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr12:48275400-48277400	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr12:48275400-48277600	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr12:48275400-48277800	Enhancers	Primary B cells from cord blood	blood
16	chr12:48275600-48277400	Enhancers	Primary hematopoietic stem cells short term culture	blood
17	chr12:48275600-48277600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr12:48275600-48277600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr12:48275600-48278000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr12:48275600-48278200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr12:48275600-48278600	Genic enhancers	NHEK	skin
22	chr12:48275600-48279800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
23	chr12:48275800-48277800	Enhancers	Placenta	Placenta
24	chr12:48275800-48278400	Enhancers	Fetal Muscle Trunk	muscle
25	chr12:48275800-48278400	Enhancers	Stomach Mucosa	stomach
26	chr12:48275800-48280000	Enhancers	Fetal Thymus	thymus
27	chr12:48276000-48277200	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr12:48276000-48277200	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
29	chr12:48276000-48277400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr12:48276000-48277400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr12:48276000-48277400	Enhancers	HSMMtube	muscle
32	chr12:48276000-48277600	Flanking Active TSS	Primary T cells from cord blood	blood
33	chr12:48276000-48277600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr12:48276000-48277600	Enhancers	Lung	lung
35	chr12:48276000-48278000	Enhancers	Sigmoid Colon	Sigmoid Colon
36	chr12:48276000-48278200	Flanking Active TSS	Duodenum Mucosa	Duodenum
37	chr12:48276200-48277400	Enhancers	Muscle Satellite Cultured Cells	--
38	chr12:48276200-48277400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr12:48276200-48277600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr12:48276200-48277600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr12:48276200-48277600	Enhancers	Osteobl	bone
42	chr12:48276200-48277800	Genic enhancers	NHLF	lung
43	chr12:48276400-48277200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
44	chr12:48276400-48277200	Enhancers	Esophagus	oesophagus
45	chr12:48276400-48277200	Enhancers	Gastric	stomach
46	chr12:48276400-48277400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr12:48276400-48277600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr12:48276400-48277600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr12:48276400-48277600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:48276400-48277600	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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