Variant report

Variant	rs541677404
Chromosome Location	chr11:85430638-85430639
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:63)
CpG islands
(count:122)
Chromatin interactive
region (count:2)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:63 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr11:85429749-85430847	A549	lung:	n/a	n/a
2	GATA3	chr11:85429736-85430735	SK-N-SH	brain:	n/a	n/a
3	FOSL2	chr11:85429852-85430727	SK-N-SH	brain:	n/a	n/a
4	EP300	chr11:85429961-85430641	A549	lung:	n/a	chr11:85430550-85430564 chr11:85430556-85430570 chr11:85430551-85430565 chr11:85430558-85430572
5	REST	chr11:85429956-85430736	PANC-1	pancreas:	n/a	n/a
6	MEF2A	chr11:85429894-85430751	SK-N-SH	brain:	n/a	chr11:85430442-85430457
7	USF1	chr11:85429876-85430655	A549	lung:	n/a	n/a
8	USF1	chr11:85430164-85430638	A549	lung:	n/a	n/a
9	FOXA2	chr11:85429629-85430654	A549	lung:	n/a	n/a
10	SP1	chr11:85430426-85430927	H1-hESC	embryonic stem cell:	n/a	n/a
11	RCOR1	chr11:85429512-85430923	IMR90	lung:	n/a	n/a
12	POLR2A	chr11:85430603-85430913	K562	blood:	n/a	n/a
13	SP1	chr11:85429809-85430729	A549	lung:	n/a	n/a
14	JUND	chr11:85429911-85430669	HCT-116	colon:	n/a	n/a
15	NFIC	chr11:85429941-85430679	SK-N-SH	brain:	n/a	n/a
16	JUND	chr11:85429852-85430719	SK-N-SH	brain:	n/a	n/a
17	TEAD4	chr11:85429866-85430738	SK-N-SH	brain:	n/a	n/a
18	NFIC	chr11:85430022-85430741	ECC-1	luminal epithelium:	n/a	n/a
19	JUND	chr11:85429828-85430756	SK-N-SH	brain:	n/a	n/a
20	FOSL1	chr11:85429979-85430654	HCT-116	colon:	n/a	n/a
21	FOSL2	chr11:85429631-85430683	A549	lung:	n/a	n/a
22	TEAD4	chr11:85429939-85430648	ECC-1	luminal epithelium:	n/a	n/a
23	RAD21	chr11:85429945-85430668	A549	lung:	n/a	chr11:85430161-85430175
24	POLR2A	chr11:85430579-85430696	Gliobla	brain:	n/a	n/a
25	NFIC	chr11:85429754-85430792	SK-N-SH	brain:	n/a	n/a
26	REST	chr11:85430558-85430858	H1-hESC	embryonic stem cell:	n/a	n/a
27	SP1	chr11:85429830-85430758	HCT-116	colon:	n/a	n/a
28	POLR2A	chr11:85429845-85430801	MCF-7	breast:	n/a	n/a
29	TEAD4	chr11:85429904-85430730	A549	lung:	n/a	n/a
30	NFIC	chr11:85430064-85430710	ECC-1	luminal epithelium:	n/a	n/a
31	TCF12	chr11:85430026-85430682	ECC-1	luminal epithelium:	n/a	n/a
32	EP300	chr11:85429760-85430735	SK-N-SH	brain:	n/a	chr11:85430550-85430564 chr11:85430556-85430570 chr11:85430551-85430565 chr11:85430558-85430572
33	TEAD4	chr11:85430431-85430924	H1-hESC	embryonic stem cell:	n/a	n/a
34	CEBPB	chr11:85429913-85430649	HCT-116	colon:	n/a	n/a
35	TEAD4	chr11:85429865-85430806	SK-N-SH	brain:	n/a	n/a
36	SP1	chr11:85429646-85430711	A549	lung:	n/a	n/a
37	FOSL2	chr11:85429944-85430658	SK-N-SH	brain:	n/a	n/a
38	PBX3	chr11:85430007-85430670	A549	lung:	n/a	n/a
39	TEAD4	chr11:85430260-85430865	H1-hESC	embryonic stem cell:	n/a	n/a
40	EP300	chr11:85429934-85430735	ECC-1	luminal epithelium:	n/a	chr11:85430550-85430564 chr11:85430556-85430570 chr11:85430551-85430565 chr11:85430558-85430572
41	MAX	chr11:85429451-85430734	A549	lung:	n/a	n/a
42	PBX3	chr11:85429887-85430726	SK-N-SH	brain:	n/a	n/a
43	RXRA	chr11:85429898-85430683	SK-N-SH	brain:	n/a	n/a
44	TCF12	chr11:85429658-85430885	SK-N-SH	brain:	n/a	n/a
45	JUND	chr11:85430115-85430733	H1-hESC	embryonic stem cell:	n/a	n/a
46	GATA3	chr11:85429781-85430723	SK-N-SH	brain:	n/a	n/a
47	EP300	chr11:85429740-85430760	SK-N-SH	brain:	n/a	chr11:85430550-85430564 chr11:85430556-85430570 chr11:85430551-85430565 chr11:85430558-85430572
48	PBX3	chr11:85429822-85430696	SK-N-SH	brain:	n/a	n/a
49	POLR2A	chr11:85429596-85430667	PANC-1	pancreas:	n/a	n/a
50	SP1	chr11:85429964-85430700	HCT-116	colon:	n/a	n/a

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

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:85430629-85430679	IMR90	lung:	fetal
2	chr11:85430634-85430684	BE2_C	brain:	n/a
3	chr11:85430629-85430679	PrEC	prostate:	n/a
4	chr11:85430634-85430684	H1-hESC	embryonic stem cell:	embryo
5	chr11:85430634-85430684	HMEC	breast:	n/a
6	chr11:85430634-85430684	ECC-1	luminal epithelium:	n/a
7	chr11:85430634-85430684	A549	lung:	n/a
8	chr11:85430629-85430679	HMEC	breast:	n/a
9	chr11:85430634-85430684	SK-N-MC	brain:	n/a
10	chr11:85430629-85430679	BJ	skin:	n/a
11	chr11:85430634-85430684	NT2-D1	testis:	n/a
12	chr11:85430629-85430679	U87	brain:	n/a
13	chr11:85430629-85430679	PANC-1	pancreas:	n/a
14	chr11:85430634-85430684	PrEC	prostate:	n/a
15	chr11:85430629-85430679	AG04449	skin:	fetal
16	chr11:85430634-85430684	MCF10A-Er-Src	breast:	n/a
17	chr11:85430629-85430679	HepG2	liver:	n/a
18	chr11:85430629-85430679	HCF	heart:	n/a
19	chr11:85430634-85430684	HNPCEpiC	eye:	n/a
20	chr11:85430634-85430684	RPTEC	kidney:	n/a
21	chr11:85430634-85430684	HRE	kidney:	n/a
22	chr11:85430634-85430684	HCT-116	colon:	n/a
23	chr11:85430629-85430679	HL-60	blood:	n/a
24	chr11:85430629-85430679	GM12878	blood:	n/a
25	chr11:85430634-85430684	HEK293	kidney:	embryo
26	chr11:85430629-85430679	Hela-S3	cervix:	n/a
27	chr11:85430634-85430684	GM06990	blood:	n/a
28	chr11:85430634-85430684	HAEpiC	amniotic membrane:	n/a
29	chr11:85430629-85430679	PFSK-1	brain:	n/a
30	chr11:85430634-85430684	HEEpiC	esophagus:	n/a
31	chr11:85430629-85430679	SK-N-MC	brain:	n/a
32	chr11:85430634-85430684	AG10803	skin:	n/a
33	chr11:85430634-85430684	MCF-7	breast:	n/a
34	chr11:85430629-85430679	Hepatocyte	liver:	n/a
35	chr11:85430629-85430679	NH-A	brain:	n/a
36	chr11:85430629-85430679	Jurkat	blood:	n/a
37	chr11:85430629-85430679	SAEC	small airway:	n/a
38	chr11:85430634-85430684	AG09309	skin:	n/a
39	chr11:85430629-85430679	NHDF-neo	bronchial:	n/a
40	chr11:85430629-85430679	NT2-D1	testis:	n/a
41	chr11:85430634-85430684	AG04449	skin:	fetal
42	chr11:85430629-85430679	BE2_C	brain:	n/a
43	chr11:85430629-85430679	HNPCEpiC	eye:	n/a
44	chr11:85430629-85430679	T-47D	breast:	n/a
45	chr11:85430634-85430684	ProgFib	skin:	n/a
46	chr11:85430629-85430679	HCT-116	colon:	n/a
47	chr11:85430634-85430684	GM19239	blood:	n/a
48	chr11:85430634-85430684	HCPEpiC	choroid plexus:	n/a
49	chr11:85430634-85430684	AG04450	lung:	fetal
50	chr11:85430629-85430679	MCF-7	breast:	n/a

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:85423310..85426529-chr11:85429130..85432198,3	MCF-7	breast:
2	chr11:85373450..85376919-chr11:85429977..85433486,3	K562	blood:

No data

Variant related genes	Relation type
SYTL2	TF binding region
SYTL2	CpG island
ENSG00000137504	Chromatin interaction
ENSG00000137501	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv468768	chr11:85395180-85436352	Weak transcription Flanking Active TSS Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv555632	chr11:85395180-85436352	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	nsv898050	chr11:85406915-85499290	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1052123	chr11:85425856-85471132	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	nsv555633	chr11:85426330-85473883	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
11	nsv1036110	chr11:85429074-85471132	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	nsv1054027	chr11:85429074-85477283	Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	esv3471508	chr11:85429687-85472395	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
14	esv3471519	chr11:85429687-85472395	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv555634	chr11:85430397-85464922	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
16	nsv555635	chr11:85430397-85470893	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:85397200-85438600	Weak transcription	Colonic Mucosa	Colon
2	chr11:85412000-85436800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr11:85412000-85438000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr11:85417600-85453000	Weak transcription	Gastric	stomach
5	chr11:85418400-85436400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr11:85422600-85448600	Weak transcription	Fetal Intestine Large	intestine
7	chr11:85422800-85448200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr11:85424000-85448600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr11:85427200-85433000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr11:85428600-85430800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
11	chr11:85428600-85431000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr11:85428600-85432000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
13	chr11:85429400-85430800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:85429400-85431000	Enhancers	HMEC	breast
15	chr11:85429400-85431200	Active TSS	Brain Anterior Caudate	brain
16	chr11:85429400-85432200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr11:85429600-85430800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr11:85429600-85430800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr11:85429600-85430800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr11:85429600-85430800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
21	chr11:85429600-85430800	Flanking Active TSS	Fetal Muscle Leg	muscle
22	chr11:85429600-85430800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
23	chr11:85429600-85432000	Strong transcription	Primary T cells from cord blood	blood
24	chr11:85429800-85430800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr11:85429800-85430800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr11:85429800-85431000	Enhancers	NHEK	skin
27	chr11:85429800-85432000	Enhancers	H1 Cell Line	embryonic stem cell
28	chr11:85430000-85430800	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr11:85430000-85430800	Enhancers	Fetal Stomach	stomach
30	chr11:85430000-85431800	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr11:85430200-85430800	Enhancers	Left Ventricle	heart
32	chr11:85430200-85431000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr11:85430200-85431200	Enhancers	Osteobl	bone
34	chr11:85430200-85431400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr11:85430200-85431800	Enhancers	NHLF	lung
36	chr11:85430200-85437800	Weak transcription	Duodenum Mucosa	Duodenum
37	chr11:85430400-85430800	Active TSS	iPS-20b Cell Line	embryonic stem cell
38	chr11:85430400-85430800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr11:85430400-85430800	Enhancers	Adipose Nuclei	Adipose
40	chr11:85430400-85430800	Enhancers	Fetal Heart	heart
41	chr11:85430400-85430800	Enhancers	Psoas Muscle	Psoas
42	chr11:85430400-85430800	Enhancers	Skeletal Muscle Male	skeletal muscle
43	chr11:85430400-85430800	Flanking Active TSS	A549	lung
44	chr11:85430400-85430800	Flanking Active TSS	NHDF-Ad	bronchial
45	chr11:85430400-85431000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:85430400-85431400	Enhancers	HUES6 Cell Line	embryonic stem cell
47	chr11:85430400-85434000	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr11:85430400-85436000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:85430400-85436600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr11:85430400-85437400	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links