Variant report

Variant	rs2044392
Chromosome Location	chr11:85522332-85522333
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:105)
CpG islands
(count:122)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:105 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:85520746-85522543	MCF-7	breast:	n/a	n/a
2	POLR2A	chr11:85521560-85522573	MCF-7	breast:	n/a	n/a
3	POLR2A	chr11:85521976-85522362	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr11:85521940-85522369	H1-hESC	embryonic stem cell:	n/a	n/a
5	EGR1	chr11:85521906-85522656	MCF-7	breast:	n/a	chr11:85522198-85522207 chr11:85522223-85522233 chr11:85522219-85522232
6	POLR2A	chr11:85521945-85522473	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr11:85522065-85522538	HepG2	liver:	n/a	n/a
8	E2F6	chr11:85521950-85522408	K562	blood:	n/a	chr11:85522224-85522233
9	TAF1	chr11:85521398-85522694	MCF-7	breast:	n/a	n/a
10	E2F6	chr11:85521767-85522923	H1-hESC	embryonic stem cell:	n/a	chr11:85522224-85522233
11	MAX	chr11:85521781-85522700	MCF-7	breast:	n/a	n/a
12	MAX	chr11:85521742-85522589	HCT-116	colon:	n/a	n/a
13	MAX	chr11:85522049-85522416	K562	blood:	n/a	n/a
14	JUND	chr11:85521896-85522460	A549	lung:	n/a	n/a
15	POLR2A	chr11:85521486-85522462	Raji	blood:	n/a	n/a
16	MAX	chr11:85522079-85522664	A549	lung:	n/a	n/a
17	POLR2A	chr11:85521923-85522417	HUVEC	blood vessel:	n/a	n/a
18	E2F6	chr11:85521864-85522784	H1-hESC	embryonic stem cell:	n/a	chr11:85522224-85522233
19	SP1	chr11:85522038-85522524	H1-hESC	embryonic stem cell:	n/a	chr11:85522222-85522234 chr11:85522222-85522234 chr11:85522223-85522233 chr11:85522224-85522233 chr11:85522290-85522301 chr11:85522223-85522232
20	POLR2A	chr11:85521919-85522359	HCT-116	colon:	n/a	n/a
21	POLR2A	chr11:85522026-85522409	A549	lung:	n/a	n/a
22	YY1	chr11:85521954-85522378	K562	blood:	n/a	chr11:85522079-85522090 chr11:85522086-85522100 chr11:85522224-85522233
23	EGR1	chr11:85521991-85522639	H1-hESC	embryonic stem cell:	n/a	chr11:85522198-85522207 chr11:85522223-85522233 chr11:85522219-85522232
24	TAF1	chr11:85521959-85522387	ECC-1	luminal epithelium:	n/a	n/a
25	POLR2A	chr11:85521955-85522520	ECC-1	luminal epithelium:	n/a	n/a
26	RAD21	chr11:85521809-85522429	H1-hESC	embryonic stem cell:	n/a	chr11:85522228-85522242
27	YY1	chr11:85521904-85522691	H1-hESC	embryonic stem cell:	n/a	chr11:85522079-85522090 chr11:85522086-85522100 chr11:85522224-85522233
28	MAX	chr11:85521850-85522626	HepG2	liver:	n/a	n/a
29	YY1	chr11:85522012-85522412	H1-hESC	embryonic stem cell:	n/a	chr11:85522079-85522090 chr11:85522086-85522100 chr11:85522224-85522233
30	MYC	chr11:85522325-85522334	MCF-7	breast:	n/a	n/a
31	TEAD4	chr11:85521915-85522511	SK-N-SH	brain:	n/a	n/a
32	IRF1	chr11:85522062-85522369	K562	blood:	n/a	chr11:85522220-85522234
33	MAX	chr11:85521772-85522663	HCT-116	colon:	n/a	n/a
34	RAD21	chr11:85522010-85522381	H1-hESC	embryonic stem cell:	n/a	chr11:85522228-85522242
35	E2F6	chr11:85521873-85522844	A549	lung:	n/a	chr11:85522224-85522233
36	TAF1	chr11:85521967-85522352	H1-hESC	embryonic stem cell:	n/a	n/a
37	CREB1	chr11:85522013-85522457	A549	lung:	n/a	n/a
38	POLR2A	chr11:85521826-85522482	Gliobla	brain:	n/a	n/a
39	MAX	chr11:85521647-85522954	A549	lung:	n/a	n/a
40	MAX	chr11:85521956-85522820	H1-hESC	embryonic stem cell:	n/a	n/a
41	MAZ	chr11:85522031-85522408	HepG2	liver:	n/a	n/a
42	EGR1	chr11:85522159-85522634	ECC-1	luminal epithelium:	n/a	chr11:85522198-85522207 chr11:85522223-85522233 chr11:85522219-85522232
43	POLR2A	chr11:85521876-85522369	SK-N-SH	brain:	n/a	n/a
44	CTCF	chr11:85522090-85522409	K562	blood:	n/a	chr11:85522232-85522245 chr11:85522226-85522239
45	SIN3AK20	chr11:85521842-85522447	PANC-1	pancreas:	n/a	n/a
46	POLR2A	chr11:85521772-85522616	PANC-1	pancreas:	n/a	n/a
47	MAX	chr11:85521755-85522695	A549	lung:	n/a	n/a
48	SIN3AK20	chr11:85519933-85522857	MCF-7	breast:	n/a	n/a
49	ZNF263	chr11:85521867-85522803	HEK293-T-REx	kidney:	n/a	n/a
50	POLR2A	chr11:85521942-85522406	A549	lung:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:85522300-85522350	SKMC	muscle:	n/a
2	chr11:85522295-85522345	BJ	skin:	n/a
3	chr11:85522295-85522345	Caco-2	colon:	n/a
4	chr11:85522295-85522345	HCM	heart:	n/a
5	chr11:85522300-85522350	SK-N-SH	brain:	n/a
6	chr11:85522300-85522350	CMK	blood:	n/a
7	chr11:85522300-85522350	Hela-S3	cervix:	n/a
8	chr11:85522300-85522350	AoSMC	blood vessel:	n/a
9	chr11:85522295-85522345	HCPEpiC	choroid plexus:	n/a
10	chr11:85522295-85522345	SK-N-SH_RA	brain:	n/a
11	chr11:85522295-85522345	HCT-116	colon:	n/a
12	chr11:85522295-85522345	PANC-1	pancreas:	n/a
13	chr11:85522300-85522350	A549	lung:	n/a
14	chr11:85522300-85522350	K562	blood:	n/a
15	chr11:85522300-85522350	AG10803	skin:	n/a
16	chr11:85522295-85522345	HAEpiC	amniotic membrane:	n/a
17	chr11:85522300-85522350	HepG2	liver:	n/a
18	chr11:85522300-85522350	LNCaP	prostate:	n/a
19	chr11:85522300-85522350	GM12892	blood:	n/a
20	chr11:85522295-85522345	HL-60	blood:	n/a
21	chr11:85522295-85522345	T-47D	breast:	n/a
22	chr11:85522300-85522350	HCPEpiC	choroid plexus:	n/a
23	chr11:85522295-85522345	HRE	kidney:	n/a
24	chr11:85522295-85522345	Jurkat	blood:	n/a
25	chr11:85522295-85522345	NB4	blood:	n/a
26	chr11:85522300-85522350	AG09319	gingival:	n/a
27	chr11:85522300-85522350	NHDF-neo	bronchial:	n/a
28	chr11:85522300-85522350	GM12891	blood:	n/a
29	chr11:85522295-85522345	HUVEC	blood vessel:	n/a
30	chr11:85522300-85522350	GM06990	blood:	n/a
31	chr11:85522300-85522350	HRE	kidney:	n/a
32	chr11:85522295-85522345	Hela-S3	cervix:	n/a
33	chr11:85522295-85522345	GM12892	blood:	n/a
34	chr11:85522295-85522345	PFSK-1	brain:	n/a
35	chr11:85522295-85522345	BE2_C	brain:	n/a
36	chr11:85522300-85522350	HEEpiC	esophagus:	n/a
37	chr11:85522295-85522345	AG09309	skin:	n/a
38	chr11:85522300-85522350	SAEC	small airway:	n/a
39	chr11:85522295-85522345	SK-N-SH	brain:	n/a
40	chr11:85522295-85522345	GM12878	blood:	n/a
41	chr11:85522295-85522345	HepG2	liver:	n/a
42	chr11:85522295-85522345	SKMC	muscle:	n/a
43	chr11:85522295-85522345	AG09319	gingival:	n/a
44	chr11:85522300-85522350	NHBE	bronchial:	n/a
45	chr11:85522295-85522345	GM19239	blood:	n/a
46	chr11:85522295-85522345	HCF	heart:	n/a
47	chr11:85522295-85522345	LNCaP	prostate:	n/a
48	chr11:85522295-85522345	ProgFib	skin:	n/a
49	chr11:85522295-85522345	HNPCEpiC	eye:	n/a
50	chr11:85522300-85522350	PrEC	prostate:	n/a

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:85374332..85377604-chr11:85518032..85524824,7	MCF-7	breast:
2	chr11:85520588..85523121-chr11:85904931..85907542,2	MCF-7	breast:
3	chr11:85520681..85523600-chr11:85778386..85780657,2	MCF-7	breast:
4	chr11:85468435..85470460-chr11:85522182..85523762,2	MCF-7	breast:
5	chr11:85371938..85377336-chr11:85519037..85522510,5	MCF-7	breast:
6	chr11:85520161..85523649-chr11:85564385..85567428,4	MCF-7	breast:
7	chr11:85434348..85438681-chr11:85520824..85523815,4	MCF-7	breast:

No data

Variant related genes	Relation type
SYTL2	TF binding region
SYTL2	CpG island
ENSG00000254502	Chromatin interaction
ENSG00000073921	Chromatin interaction
ENSG00000150676	Chromatin interaction
ENSG00000137501	Chromatin interaction
ENSG00000215504	Chromatin interaction
ENSG00000137504	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10898406	0.90[ASN][1000 genomes]
rs10898410	0.87[ASN][1000 genomes]
rs10898413	0.87[ASN][1000 genomes]
rs10898415	0.91[ASN][1000 genomes]
rs11606656	0.93[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12362853	0.90[ASN][1000 genomes]
rs1445497	0.92[ASN][1000 genomes]
rs1481700	0.87[ASN][1000 genomes]
rs2008890	0.87[ASN][1000 genomes]
rs2044391	0.92[ASN][1000 genomes]
rs2374683	0.87[ASN][1000 genomes]
rs485485	0.87[ASN][1000 genomes]
rs493078	0.86[ASN][1000 genomes]
rs4944538	0.87[ASN][1000 genomes]
rs556918	0.90[ASN][1000 genomes]
rs630613	0.85[ASN][1000 genomes]
rs644972	0.85[ASN][1000 genomes]
rs652615	0.86[ASN][1000 genomes]
rs667275	0.86[ASN][1000 genomes]
rs683105	0.87[ASN][1000 genomes]
rs7103790	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7123846	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051155	chr11:85006564-85721261	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
2	nsv541110	chr11:85006564-85721261	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	esv2758279	chr11:85180480-85603988	Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	esv2759845	chr11:85180480-85603988	Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
5	nsv832222	chr11:85405712-85603981	Enhancers Active TSS Bivalent Enhancer Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv1047147	chr11:85459235-85594800	Flanking Active TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
7	nsv541114	chr11:85459235-85594800	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	esv2762927	chr11:85468051-85559618	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1052737	chr11:85477084-85554914	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv541115	chr11:85477084-85554914	Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	nsv1049630	chr11:85486866-85535123	Enhancers Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1035489	chr11:85502953-85778229	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2044392	SYTL2	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85520000-85522400	Active TSS	Stomach Mucosa	stomach
2	chr11:85520400-85522600	Enhancers	Fetal Brain Male	brain
3	chr11:85520400-85522800	Bivalent/Poised TSS	Thymus	Thymus
4	chr11:85520600-85522600	Active TSS	NHDF-Ad	bronchial
5	chr11:85520600-85523600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr11:85520800-85522600	Active TSS	Esophagus	oesophagus
7	chr11:85520800-85522800	Active TSS	Fetal Kidney	kidney
8	chr11:85520800-85523000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
9	chr11:85521000-85522600	Active TSS	Left Ventricle	heart
10	chr11:85521000-85522800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:85521000-85522800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr11:85521000-85522800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr11:85521000-85522800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr11:85521000-85522800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:85521000-85522800	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
16	chr11:85521000-85523000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
17	chr11:85521000-85523000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
18	chr11:85521200-85522400	Active TSS	Small Intestine	intestine
19	chr11:85521200-85522800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
20	chr11:85521200-85522800	Flanking Active TSS	Primary hematopoietic stem cells	blood
21	chr11:85521200-85522800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
22	chr11:85521200-85522800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:85521200-85522800	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr11:85521200-85522800	Active TSS	Ovary	ovary
25	chr11:85521200-85522800	Active TSS	NHLF	lung
26	chr11:85521200-85523000	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
27	chr11:85521400-85522600	Active TSS	Primary T helper naive cells from peripheral blood	blood
28	chr11:85521400-85522600	Active TSS	Primary T killer memory cells from peripheral blood	blood
29	chr11:85521400-85522600	Active TSS	Brain Substantia Nigra	brain
30	chr11:85521400-85522800	Flanking Active TSS	Primary B cells from cord blood	blood
31	chr11:85521400-85522800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr11:85521600-85522400	Active TSS	Rectal Mucosa Donor 29	rectum
33	chr11:85521600-85522400	Active TSS	Rectal Mucosa Donor 31	rectum
34	chr11:85521600-85522600	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:85521600-85522800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
36	chr11:85521600-85522800	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr11:85521600-85522800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr11:85521600-85522800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
39	chr11:85521600-85522800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr11:85521600-85522800	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr11:85521600-85522800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr11:85521600-85522800	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr11:85521600-85523000	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
44	chr11:85521600-85523000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
45	chr11:85521600-85525000	Weak transcription	Hela-S3	cervix
46	chr11:85521800-85522400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
47	chr11:85521800-85522400	Active TSS	Primary T helper cells PMA-I stimulated	--
48	chr11:85521800-85522400	Active TSS	Spleen	Spleen
49	chr11:85521800-85522600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr11:85521800-85522600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood

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