Variant report

Variant	rs2649666
Chromosome Location	chr11:57283056-57283057
allele	C/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	chr11:57281090-57283641	HL-60	blood:	n/a	n/a
2	TBP	chr11:57281817-57283531	K562	blood:	n/a	n/a
3	UBTF	chr11:57281466-57283773	K562	blood:	n/a	n/a
4	TCF7L2	chr11:57282755-57283524	HCT-116	colon:	n/a	n/a
5	MAX	chr11:57283041-57283738	SK-N-SH	brain:	n/a	chr11:57283229-57283239
6	TAF1	chr11:57283007-57283335	PFSK-1	brain:	n/a	n/a
7	MXI1	chr11:57282580-57283673	K562	blood:	n/a	n/a
8	UBTF	chr11:57281627-57283578	K562	blood:	n/a	n/a
9	ZBTB7A	chr11:57281914-57283531	K562	blood:	n/a	chr11:57282888-57282897 chr11:57283394-57283403
10	EGR1	chr11:57282092-57283425	K562	blood:	n/a	chr11:57282900-57282911 chr11:57282900-57282910 chr11:57283231-57283241 chr11:57282899-57282912 chr11:57283017-57283026 chr11:57282899-57282912 chr11:57282900-57282909 chr11:57282681-57282690 chr11:57282888-57282901 chr11:57282900-57282911 chr11:57283232-57283245 chr11:57283229-57283239 chr11:57282889-57282899 chr11:57282896-57282910 chr11:57283226-57283239 chr11:57282899-57282912 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282898-57282912
11	POLR2A	chr11:57282697-57283080	H1-neurons	neurons:	n/a	n/a
12	MAX	chr11:57282917-57283589	K562	blood:	n/a	chr11:57283229-57283239
13	FOXA2	chr11:57282855-57283537	A549	lung:	n/a	n/a
14	FOXP2	chr11:57282922-57283390	PFSK-1	brain:	n/a	n/a
15	SIN3AK20	chr11:57283048-57283385	HepG2	liver:	n/a	n/a
16	POLR2A	chr11:57282039-57283575	K562	blood:	n/a	n/a
17	POLR2A	chr11:57281720-57283555	GM12878	blood:	n/a	n/a
18	EGR1	chr11:57282214-57283383	K562	blood:	n/a	chr11:57282900-57282911 chr11:57282900-57282910 chr11:57283231-57283241 chr11:57282899-57282912 chr11:57283017-57283026 chr11:57282899-57282912 chr11:57282900-57282909 chr11:57282681-57282690 chr11:57282888-57282901 chr11:57282900-57282911 chr11:57283232-57283245 chr11:57283229-57283239 chr11:57282889-57282899 chr11:57282896-57282910 chr11:57283226-57283239 chr11:57282899-57282912 chr11:57282900-57282910 chr11:57282899-57282912 chr11:57282898-57282912
19	POLR2A	chr11:57281645-57283571	K562	blood:	n/a	n/a
20	TCF12	chr11:57282921-57283439	A549	lung:	n/a	n/a
21	POLR2A	chr11:57281888-57283712	PFSK-1	brain:	n/a	n/a
22	POLR2A	chr11:57281402-57283699	K562	blood:	n/a	n/a
23	POLR2A	chr11:57282841-57283392	HepG2	liver:	n/a	n/a
24	USF1	chr11:57283015-57283535	H1-hESC	embryonic stem cell:	n/a	chr11:57283281-57283290 chr11:57283279-57283290 chr11:57283280-57283289 chr11:57283280-57283289
25	JUND	chr11:57282059-57283437	K562	blood:	n/a	chr11:57282388-57282397
26	POLR2A	chr11:57282874-57283608	HepG2	liver:	n/a	n/a
27	POLR2A	chr11:57281594-57283512	GM18951	blood:	n/a	n/a
28	HMGN3	chr11:57281508-57283551	K562	blood:	n/a	n/a
29	SIN3AK20	chr11:57282813-57283392	K562	blood:	n/a	n/a
30	BHLHE40	chr11:57281148-57283762	K562	blood:	n/a	chr11:57282437-57282453 chr11:57283281-57283290 chr11:57283280-57283289 chr11:57282445-57282461 chr11:57283280-57283289 chr11:57282434-57282450 chr11:57282427-57282443
31	JUN	chr11:57282909-57283175	H1-hESC	embryonic stem cell:	n/a	n/a
32	TAF1	chr11:57281700-57283402	HepG2	liver:	n/a	n/a
33	USF1	chr11:57283056-57283534	K562	blood:	n/a	chr11:57283281-57283290 chr11:57283279-57283290 chr11:57283280-57283289 chr11:57283280-57283289
34	POLR2A	chr11:57283039-57283415	MCF-7	breast:	n/a	n/a
35	POLR2A	chr11:57283041-57283439	MCF-7	breast:	n/a	n/a
36	POLR2A	chr11:57281596-57283522	GM18505	blood:	n/a	n/a
37	POLR2A	chr11:57282809-57283364	GM12892	blood:	n/a	n/a
38	CBX3	chr11:57282793-57283406	K562	blood:	n/a	n/a
39	POLR2A	chr11:57282710-57283658	HUVEC	blood vessel:	n/a	n/a
40	CTCF	chr11:57282980-57283130	GM12865	blood:	n/a	n/a
41	MAX	chr11:57282934-57283529	H1-hESC	embryonic stem cell:	n/a	chr11:57283229-57283239
42	MAX	chr11:57282795-57283671	A549	lung:	n/a	chr11:57283229-57283239
43	CTBP2	chr11:57281662-57283440	H1-hESC	embryonic stem cell:	n/a	n/a
44	POLR2A	chr11:57282969-57283565	HCT-116	colon:	n/a	n/a
45	MAX	chr11:57282773-57283636	SK-N-SH	brain:	n/a	chr11:57283229-57283239
46	ZBTB7A	chr11:57282653-57283644	ECC-1	luminal epithelium:	n/a	chr11:57282888-57282897 chr11:57283394-57283403
47	SIN3A	chr11:57281214-57283753	H1-hESC	embryonic stem cell:	n/a	chr11:57281841-57281852 chr11:57281954-57281965
48	POLR2A	chr11:57282653-57283375	GM12878	blood:	n/a	n/a
49	MYC	chr11:57281401-57283820	K562	blood:	n/a	chr11:57282432-57282442 chr11:57283229-57283239
50	MYBL2	chr11:57282903-57283653	HepG2	liver:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:57283055-57283105	SKMC	muscle:	n/a
2	chr11:57283055-57283105	ECC-1	luminal epithelium:	n/a
3	chr11:57283055-57283105	NT2-D1	testis:	n/a
4	chr11:57283055-57283105	AG09319	gingival:	n/a
5	chr11:57283055-57283105	SK-N-MC	brain:	n/a
6	chr11:57283055-57283105	AoSMC	blood vessel:	n/a
7	chr11:57283055-57283105	HEK293	kidney:	embryo
8	chr11:57283055-57283105	SK-N-SH	brain:	n/a
9	chr11:57283055-57283105	RPTEC	kidney:	n/a
10	chr11:57283055-57283105	SK-N-SH_RA	brain:	n/a
11	chr11:57283055-57283105	GM19239	blood:	n/a
12	chr11:57283055-57283105	CMK	blood:	n/a
13	chr11:57283055-57283105	ovcar-3	ovarian:	n/a
14	chr11:57283055-57283105	HRPEpiC	eye:	n/a
15	chr11:57283055-57283105	LNCaP	prostate:	n/a
16	chr11:57283055-57283105	Jurkat	blood:	n/a
17	chr11:57283055-57283105	SAEC	small airway:	n/a
18	chr11:57283055-57283105	HIPEpiC	eye:	n/a
19	chr11:57283055-57283105	AG10803	skin:	n/a
20	chr11:57283055-57283105	HCPEpiC	choroid plexus:	n/a
21	chr11:57283055-57283105	BE2_C	brain:	n/a
22	chr11:57283055-57283105	HepG2	liver:	n/a
23	chr11:57283055-57283105	GM06990	blood:	n/a
24	chr11:57283055-57283105	HRE	kidney:	n/a
25	chr11:57283055-57283105	NB4	blood:	n/a
26	chr11:57283055-57283105	NH-A	brain:	n/a
27	chr11:57283055-57283105	PFSK-1	brain:	n/a
28	chr11:57283055-57283105	PrEC	prostate:	n/a
29	chr11:57283055-57283105	HCM	heart:	n/a
30	chr11:57283055-57283105	Hela-S3	cervix:	n/a
31	chr11:57283055-57283105	T-47D	breast:	n/a
32	chr11:57283055-57283105	HPAEpiC	pulmonary alveolar:	n/a
33	chr11:57283055-57283105	BJ	skin:	n/a
34	chr11:57283055-57283105	HEEpiC	esophagus:	n/a
35	chr11:57283055-57283105	HCT-116	colon:	n/a
36	chr11:57283055-57283105	NHDF-neo	bronchial:	n/a
37	chr11:57283055-57283105	AG09309	skin:	n/a
38	chr11:57283055-57283105	U87	brain:	n/a
39	chr11:57283055-57283105	K562	blood:	n/a
40	chr11:57283055-57283105	AG04449	skin:	fetal
41	chr11:57283055-57283105	Caco-2	colon:	n/a
42	chr11:57283055-57283105	ProgFib	skin:	n/a
43	chr11:57283055-57283105	AG04450	lung:	fetal
44	chr11:57283055-57283105	MCF10A-Er-Src	breast:	n/a
45	chr11:57283055-57283105	MCF-7	breast:	n/a
46	chr11:57283055-57283105	NHBE	bronchial:	n/a
47	chr11:57283055-57283105	HNPCEpiC	eye:	n/a
48	chr11:57283055-57283105	HRCEpiC	kidney:	n/a
49	chr11:57283055-57283105	PANC-1	pancreas:	n/a
50	chr11:57283055-57283105	A549	lung:	n/a

No.	Distal block	Cell Line	Cell type
1	chr11:57095142..57097690-chr11:57281751..57283331,2	K562	blood:
2	chr11:57282855..57283355-chr6:97284984..97285522,2	HCT-116	colon:
3	chr11:57279697..57283964-chr11:57296063..57300992,5	K562	blood:
4	chr11:57260838..57262632-chr11:57281221..57283072,2	K562	blood:
5	chr11:57264825..57270955-chr11:57280277..57284813,10	K562	blood:
6	chr11:57265680..57269520-chr11:57278275..57283954,6	K562	blood:
7	chr11:57102611..57104475-chr11:57280670..57283217,2	K562	blood:
8	chr11:57279377..57284601-chr11:57296598..57300992,7	K562	blood:

Variant related genes	Relation type
SLC43A1	TF binding region
SLC43A1	CpG island
ENSG00000149150	Chromatin interaction
ENSG00000134809	Chromatin interaction
ENSG00000149136	Chromatin interaction
ENSG00000112218	Chromatin interaction
ENSG00000238692	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1124942	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12223229	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2234409	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2467328	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2467329	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2467330	0.81[EUR][1000 genomes]
rs2581930	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2649644	0.81[EUR][1000 genomes]
rs2649645	0.81[EUR][1000 genomes]
rs2649649	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2649651	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2649653	0.83[EUR][1000 genomes]
rs2649655	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2649656	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2649658	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2649659	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2729358	0.81[EUR][1000 genomes]
rs2729359	0.81[EUR][1000 genomes]
rs2729367	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2729368	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2729369	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2729370	0.89[EUR][1000 genomes]
rs2729373	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2729375	0.86[EUR][1000 genomes]
rs2729382	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2848621	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2848622	0.81[EUR][1000 genomes]
rs2848624	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2848638	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2848639	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs514385	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs722823	0.90[AMR][1000 genomes];0.90[EUR][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	nsv1044030	chr11:57073395-58035564	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv541047	chr11:57073395-58035564	Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv530621	chr11:57139699-57703639	Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2649666	SMTNL1	cis	lung	GTEx
rs2649666	SMTNL1	cis	Artery Tibial	GTEx
rs2649666	SMTNL1	cis	Nerve Tibial	GTEx
rs2649666	SMTNL1	cis	Esophagus Muscularis	GTEx
rs2649666	TIMM10	Cis_1M	lymphoblastoid	RTeQTL
rs2649666	SMTNL1	cis	Thyroid	GTEx
rs2649666	SMTNL1	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:57280400-57283600	Active TSS	Pancreas	Pancrea
2	chr11:57280600-57284000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
3	chr11:57280600-57284000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
4	chr11:57280800-57283800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr11:57281000-57284000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
6	chr11:57281200-57283400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr11:57281200-57283600	Active TSS	Pancreatic Islets	Pancreatic Islet
8	chr11:57281200-57283800	Flanking Active TSS	Primary hematopoietic stem cells	blood
9	chr11:57281200-57284000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
10	chr11:57281200-57284000	Active TSS	GM12878-XiMat	blood
11	chr11:57281400-57283200	Active TSS	Brain Cingulate Gyrus	brain
12	chr11:57281400-57283400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr11:57281400-57283400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr11:57281400-57283400	Active TSS	Ovary	ovary
15	chr11:57281400-57283400	Active TSS	Rectal Smooth Muscle	rectum
16	chr11:57281400-57283600	Active TSS	H9 Cell Line	embryonic stem cell
17	chr11:57281400-57283600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
18	chr11:57281400-57283600	Active TSS	Primary T cells from cord blood	blood
19	chr11:57281400-57283600	Active TSS	Left Ventricle	heart
20	chr11:57281400-57283600	Active TSS	NHLF	lung
21	chr11:57281400-57283800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
22	chr11:57281400-57283800	Active TSS	Right Ventricle	heart
23	chr11:57281400-57284000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:57281600-57283200	Active TSS	Brain Substantia Nigra	brain
25	chr11:57281600-57283400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr11:57281600-57283400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:57281600-57283400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr11:57281600-57283400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
29	chr11:57281600-57283400	Bivalent Enhancer	Fetal Brain Male	brain
30	chr11:57281600-57283400	Active TSS	Psoas Muscle	Psoas
31	chr11:57281600-57283600	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr11:57281600-57283600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:57281600-57283600	Active TSS	Muscle Satellite Cultured Cells	--
34	chr11:57281600-57283600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
35	chr11:57281600-57283600	Flanking Active TSS	Colonic Mucosa	Colon
36	chr11:57281600-57283600	Active TSS	Colon Smooth Muscle	Colon
37	chr11:57281600-57283800	Active TSS	Brain Anterior Caudate	brain
38	chr11:57281600-57283800	Active TSS	Right Atrium	heart
39	chr11:57281600-57283800	Active TSS	HSMM	muscle
40	chr11:57281600-57284000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr11:57281600-57284000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
42	chr11:57281800-57283200	Active TSS	Gastric	stomach
43	chr11:57281800-57283400	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr11:57281800-57283400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr11:57281800-57283400	Active TSS	Liver	Liver
46	chr11:57281800-57283400	Active TSS	Small Intestine	intestine
47	chr11:57281800-57283600	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr11:57281800-57283600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr11:57281800-57283600	Active TSS	Aorta	Aorta
50	chr11:57281800-57283600	Active TSS	Brain Angular Gyrus	brain

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