Variant report

Variant	rs211109
Chromosome Location	chr11:18034198-18034199
allele	A/C/G/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	MAX	chr11:18033779-18035578	HCT-116	colon:	n/a	chr11:18034746-18034756
2	POLR2A	chr11:18033734-18035340	H1-hESC	embryonic stem cell:	n/a	n/a
3	TFAP2C	chr11:18034014-18035344	Hela-S3	cervix:	n/a	chr11:18034719-18034734
4	CREB1	chr11:18033726-18035310	HepG2	liver:	n/a	n/a
5	MAX	chr11:18033824-18035566	A549	lung:	n/a	chr11:18034746-18034756
6	SIN3AK20	chr11:18034154-18035224	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr11:18033920-18035400	GM15510	blood:	n/a	n/a
8	ZNF263	chr11:18033468-18034568	HEK293-T-REx	kidney:	n/a	n/a
9	POLR2A	chr11:18033518-18035690	Raji	blood:	n/a	n/a
10	CHD2	chr11:18033851-18035296	GM12878	blood:	n/a	chr11:18034660-18034670
11	MXI1	chr11:18033557-18035557	IMR90	lung:	n/a	n/a
12	ZEB1	chr11:18034192-18034835	GM12878	blood:	n/a	n/a
13	PML	chr11:18034164-18035277	GM12878	blood:	n/a	n/a
14	POLR2A	chr11:18034087-18035589	GM19099	blood:	n/a	n/a
15	POLR2A	chr11:18033557-18035404	H1-neurons	neurons:	n/a	n/a
16	POLR2A	chr11:18033844-18035506	Hela-S3	cervix:	n/a	n/a
17	TBP	chr11:18034017-18034788	H1-hESC	embryonic stem cell:	n/a	n/a
18	EGR1	chr11:18034128-18035364	HCT-116	colon:	n/a	chr11:18034518-18034532 chr11:18034746-18034756 chr11:18034745-18034755 chr11:18034592-18034605 chr11:18034593-18034607 chr11:18034475-18034488 chr11:18034588-18034610 chr11:18034592-18034605 chr11:18034595-18034604
19	MTA3	chr11:18033920-18034527	GM12878	blood:	n/a	n/a
20	POLR2A	chr11:18034144-18035282	GM12878	blood:	n/a	n/a
21	POLR2A	chr11:18034077-18035427	GM18951	blood:	n/a	n/a
22	MAZ	chr11:18033827-18035177	HepG2	liver:	n/a	chr11:18034746-18034756
23	POLR2A	chr11:18034184-18035290	ECC-1	luminal epithelium:	n/a	n/a
24	MXI1	chr11:18033813-18035235	HepG2	liver:	n/a	n/a
25	UBTF	chr11:18033311-18035366	K562	blood:	n/a	n/a
26	POLR2A	chr11:18034129-18035236	U87	brain:	n/a	n/a
27	SIN3A	chr11:18033698-18035726	H1-hESC	embryonic stem cell:	n/a	chr11:18034430-18034441 chr11:18034403-18034414 chr11:18034428-18034441
28	EGR1	chr11:18034181-18035423	HCT-116	colon:	n/a	chr11:18034518-18034532 chr11:18034746-18034756 chr11:18034745-18034755 chr11:18034592-18034605 chr11:18034593-18034607 chr11:18034475-18034488 chr11:18034588-18034610 chr11:18034592-18034605 chr11:18034595-18034604
29	POLR2A	chr11:18034182-18035034	HUVEC	blood vessel:	n/a	n/a
30	POLR2A	chr11:18034110-18035331	GM19193	blood:	n/a	n/a
31	POLR2A	chr11:18034128-18034203	H1-hESC	embryonic stem cell:	n/a	n/a
32	RCOR1	chr11:18033311-18035931	IMR90	lung:	n/a	n/a
33	RUNX3	chr11:18034184-18035368	GM12878	blood:	n/a	n/a
34	POLR2A	chr11:18032592-18035146	HepG2	liver:	n/a	n/a
35	UBTF	chr11:18033775-18034966	K562	blood:	n/a	n/a
36	POLR2A	chr11:18034180-18035152	GM12892	blood:	n/a	n/a
37	MAX	chr11:18033204-18035353	K562	blood:	n/a	chr11:18034746-18034756
38	MAX	chr11:18033742-18035873	NB4	blood:	n/a	chr11:18034746-18034756
39	MXI1	chr11:18034008-18035239	GM12878	blood:	n/a	n/a
40	HA-E2F1	chr11:18033723-18035559	MCF-7	breast:	n/a	chr11:18034322-18034331 chr11:18034319-18034331 chr11:18034601-18034611
41	POLR2A	chr11:18034195-18035333	NB4	blood:	n/a	n/a
42	CHD2	chr11:18033964-18035084	HepG2	liver:	n/a	chr11:18034660-18034670
43	POLR2A	chr11:18033503-18035427	GM12878	blood:	n/a	n/a
44	TAF1	chr11:18034110-18035082	ECC-1	luminal epithelium:	n/a	n/a
45	TFAP2A	chr11:18033751-18035220	Hela-S3	cervix:	n/a	chr11:18034813-18034828 chr11:18034475-18034486 chr11:18034689-18034700 chr11:18034226-18034237 chr11:18034226-18034237 chr11:18034475-18034486 chr11:18034688-18034700 chr11:18034719-18034734 chr11:18034722-18034730 chr11:18034226-18034237 chr11:18034476-18034484 chr11:18034719-18034731 chr11:18034475-18034486 chr11:18034690-18034705 chr11:18034226-18034237 chr11:18034476-18034484 chr11:18034475-18034487 chr11:18034565-18034577 chr11:18034476-18034484
46	POLR2A	chr11:18033952-18035465	GM18505	blood:	n/a	n/a
47	POLR2A	chr11:18034096-18035365	SK-N-MC	brain:	n/a	n/a
48	MYC	chr11:18032582-18035024	K562	blood:	n/a	chr11:18034746-18034756
49	TAF1	chr11:18033828-18035249	HepG2	liver:	n/a	n/a
50	CCNT2	chr11:18033938-18035241	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:18032918..18034516-chr11:18609753..18611706,2	MCF-7	breast:
2	chr11:18034017..18034785-chr7:128049172..128050147,2	NB4	blood:
3	chr11:18034152..18035903-chr11:18125561..18127722,2	MCF-7	breast:
4	chr11:17228155..17229875-chr11:18033843..18035455,2	K562	blood:
5	chr11:18024725..18026485-chr11:18033759..18035414,2	MCF-7	breast:
6	chr10:123687232..123687760-chr11:18034020..18034616,2	HCT-116	colon:
7	chr11:18033853..18039770-chr11:18040771..18045725,5	K562	blood:
8	chr11:18033935..18034483-chr6:41748410..41748911,2	HCT-116	colon:
9	chr11:18033238..18034907-chr11:18042629..18045446,2	MCF-7	breast:

Variant related genes	Relation type
SERGEF	TF binding region
ENSG00000011405	Chromatin interaction
ENSG00000107669	Chromatin interaction
ENSG00000151116	Chromatin interaction
ENSG00000129158	Chromatin interaction
ENSG00000129167	Chromatin interaction
ENSG00000070081	Chromatin interaction
ENSG00000166788	Chromatin interaction
ENSG00000124593	Chromatin interaction
ENSG00000255448	Chromatin interaction
ENSG00000106348	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10488682	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10832871	0.90[AFR][1000 genomes]
rs10832875	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10832876	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11024445	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11024449	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11575890	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs172423	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs211104	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs211105	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2299626	0.90[AFR][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs211109	SERGEF	cis	Muscle Skeletal	GTEx
rs211109	SAAL1	cis	Artery Tibial	GTEx
rs211109	SAAL1	cis	lung	GTEx
rs211109	SERGEF	cis	Adipose Subcutaneous	GTEx
rs211109	SAAL1	Cis_1M	lymphoblastoid	RTeQTL
rs211109	RP1-59M18.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:18033200-18034200	Flanking Active TSS	Brain Germinal Matrix	brain
2	chr11:18033200-18034200	Flanking Active TSS	Dnd41	blood
3	chr11:18033200-18034200	Flanking Active TSS	Hela-S3	cervix
4	chr11:18033200-18034200	Flanking Active TSS	HMEC	breast
5	chr11:18033200-18035200	Bivalent/Poised TSS	HepG2	liver
6	chr11:18033200-18035600	Active TSS	Brain Substantia Nigra	brain
7	chr11:18033400-18034200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr11:18033400-18034200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
9	chr11:18033400-18034200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr11:18033400-18034200	Flanking Active TSS	Fetal Brain Female	brain
11	chr11:18033400-18034200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
12	chr11:18033400-18034200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr11:18033400-18034200	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr11:18033400-18035800	Active TSS	Pancreatic Islets	Pancreatic Islet
15	chr11:18033400-18036000	Active TSS	Rectal Smooth Muscle	rectum
16	chr11:18033600-18034200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr11:18033600-18034200	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr11:18033600-18034200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
19	chr11:18033600-18034200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr11:18033600-18034200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
21	chr11:18033600-18034200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:18033600-18034200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:18033600-18034200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr11:18033600-18034200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr11:18033600-18034200	Flanking Active TSS	Liver	Liver
26	chr11:18033600-18034200	Flanking Active TSS	Right Ventricle	heart
27	chr11:18033600-18034200	Flanking Active TSS	HUVEC	blood vessel
28	chr11:18033600-18034200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
29	chr11:18033600-18034400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr11:18033600-18035200	Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr11:18033600-18035400	Active TSS	Brain Hippocampus Middle	brain
32	chr11:18033600-18035400	Active TSS	Colon Smooth Muscle	Colon
33	chr11:18033600-18035400	Active TSS	Fetal Intestine Large	intestine
34	chr11:18033600-18035400	Active TSS	Stomach Mucosa	stomach
35	chr11:18033600-18035400	Active TSS	Thymus	Thymus
36	chr11:18033600-18035400	Active TSS	HSMMtube	muscle
37	chr11:18033600-18035600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr11:18033600-18035600	Active TSS	H9 Cell Line	embryonic stem cell
39	chr11:18033600-18035800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr11:18033800-18034200	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr11:18033800-18034200	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
42	chr11:18033800-18034200	Flanking Active TSS	Primary B cells from peripheral blood	blood
43	chr11:18033800-18034200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr11:18033800-18034200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
45	chr11:18033800-18034200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr11:18033800-18034200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr11:18033800-18034200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
48	chr11:18033800-18034200	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
49	chr11:18033800-18034200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr11:18033800-18034200	Flanking Active TSS	Adipose Nuclei	Adipose

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