Variant report

Variant	rs2254388
Chromosome Location	chr11:65837599-65837600
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:223)
CpG islands
(count:61)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:223 , 50 per page) page: 1 2 3 4 5

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:65836889-65838227	ProgFib	skin:	n/a	n/a
2	SP1	chr11:65837365-65837916	GM12878	blood:	n/a	chr11:65837734-65837744 chr11:65837544-65837558 chr11:65837407-65837419 chr11:65837408-65837418 chr11:65837734-65837744
3	RUNX3	chr11:65836229-65837957	GM12878	blood:	n/a	n/a
4	MAX	chr11:65836371-65838975	A549	lung:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
5	ZBTB7A	chr11:65837200-65838621	K562	blood:	n/a	n/a
6	POLR2A	chr11:65837107-65838167	HUVEC	blood vessel:	n/a	n/a
7	TCF3	chr11:65837218-65838024	GM12878	blood:	n/a	n/a
8	HEY1	chr11:65837333-65838021	K562	blood:	n/a	chr11:65837450-65837465
9	ETS1	chr11:65837134-65838343	K562	blood:	n/a	chr11:65837233-65837246
10	POLR2A	chr11:65836330-65837671	GM12878	blood:	n/a	n/a
11	MAX	chr11:65837369-65837939	GM12878	blood:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
12	STAT5A	chr11:65835763-65837684	GM12878	blood:	n/a	n/a
13	MAX	chr11:65837319-65837923	HepG2	liver:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
14	MYC	chr11:65837494-65837964	MCF-7	breast:	n/a	chr11:65837642-65837651
15	NFATC1	chr11:65836618-65837780	GM12878	blood:	n/a	n/a
16	CCNT2	chr11:65837208-65838564	K562	blood:	n/a	n/a
17	ZBTB7A	chr11:65837106-65837673	ECC-1	luminal epithelium:	n/a	n/a
18	BHLHE40	chr11:65837450-65837880	GM12878	blood:	n/a	n/a
19	POLR2A	chr11:65837187-65838778	HUVEC	blood vessel:	n/a	n/a
20	MAX	chr11:65837349-65838032	SK-N-SH	brain:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
21	PBX3	chr11:65836815-65837949	SK-N-SH	brain:	n/a	n/a
22	NFIC	chr11:65837376-65838544	ECC-1	luminal epithelium:	n/a	n/a
23	EBF1	chr11:65837426-65837660	GM12878	blood:	n/a	n/a
24	POLR2A	chr11:65837284-65837987	GM10847	blood:	n/a	n/a
25	POLR2A	chr11:65836624-65837689	U87	brain:	n/a	n/a
26	JUND	chr11:65837169-65838077	A549	lung:	n/a	n/a
27	MAX	chr11:65836771-65838506	HepG2	liver:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
28	EGR1	chr11:65837319-65837840	ECC-1	luminal epithelium:	n/a	chr11:65837815-65837824 chr11:65837814-65837823 chr11:65837549-65837562 chr11:65837717-65837731 chr11:65837549-65837562
29	PBX3	chr11:65837312-65837801	A549	lung:	n/a	n/a
30	HMGN3	chr11:65837263-65838575	K562	blood:	n/a	n/a
31	FOSL2	chr11:65837075-65837672	HepG2	liver:	n/a	n/a
32	TCF12	chr11:65837057-65838143	ECC-1	luminal epithelium:	n/a	n/a
33	CHD2	chr11:65837356-65837913	Hela-S3	cervix:	n/a	n/a
34	POLR2A	chr11:65837320-65837668	GM12891	blood:	n/a	n/a
35	POLR2A	chr11:65837206-65838200	A549	lung:	n/a	n/a
36	ELF1	chr11:65837199-65837668	HepG2	liver:	n/a	chr11:65837339-65837351
37	POLR2A	chr11:65836928-65838009	GM15510	blood:	n/a	n/a
38	TAF1	chr11:65837294-65838100	ECC-1	luminal epithelium:	n/a	n/a
39	POLR2A	chr11:65836338-65838105	GM12891	blood:	n/a	n/a
40	SIN3AK20	chr11:65837532-65837838	HepG2	liver:	n/a	n/a
41	MAZ	chr11:65836170-65839866	IMR90	lung:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
42	POLR2A	chr11:65836351-65837681	K562	blood:	n/a	n/a
43	MYC	chr11:65837488-65838276	K562	blood:	n/a	chr11:65837642-65837651
44	MYC	chr11:65837413-65838452	MCF-7	breast:	n/a	chr11:65837642-65837651 chr11:65837468-65837478
45	MXI1	chr11:65837443-65837955	GM12878	blood:	n/a	n/a
46	POLR2A	chr11:65836498-65837980	GM12891	blood:	n/a	n/a
47	SIN3A	chr11:65836824-65838298	H1-hESC	embryonic stem cell:	n/a	n/a
48	RELA	chr11:65836431-65837831	GM12891	blood:	n/a	n/a
49	HDAC2	chr11:65837098-65838011	MCF-7	breast:	n/a	chr11:65837813-65837822
50	POLR2A	chr11:65836645-65838021	GM19099	blood:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr11:65837595-65837645	HEK293	kidney:	embryo
2	chr11:65837595-65837645	AG09319	gingival:	n/a
3	chr11:65837595-65837645	HCM	heart:	n/a
4	chr11:65837595-65837645	AG04450	lung:	fetal
5	chr11:65837595-65837645	SK-N-MC	brain:	n/a
6	chr11:65837595-65837645	SK-N-SH	brain:	n/a
7	chr11:65837595-65837645	HRE	kidney:	n/a
8	chr11:65837595-65837645	GM12878	blood:	n/a
9	chr11:65837595-65837645	MCF10A-Er-Src	breast:	n/a
10	chr11:65837595-65837645	NB4	blood:	n/a
11	chr11:65837595-65837645	HMEC	breast:	n/a
12	chr11:65837595-65837645	BJ	skin:	n/a
13	chr11:65837595-65837645	H1-hESC	embryonic stem cell:	embryo
14	chr11:65837595-65837645	LNCaP	prostate:	n/a
15	chr11:65837595-65837645	SK-N-SH_RA	brain:	n/a
16	chr11:65837595-65837645	HRPEpiC	eye:	n/a
17	chr11:65837595-65837645	HL-60	blood:	n/a
18	chr11:65837595-65837645	PrEC	prostate:	n/a
19	chr11:65837595-65837645	AG10803	skin:	n/a
20	chr11:65837595-65837645	HNPCEpiC	eye:	n/a
21	chr11:65837595-65837645	GM12892	blood:	n/a
22	chr11:65837595-65837645	HPAEpiC	pulmonary alveolar:	n/a
23	chr11:65837595-65837645	HepG2	liver:	n/a
24	chr11:65837595-65837645	AG04449	skin:	fetal
25	chr11:65837595-65837645	HUVEC	blood vessel:	n/a
26	chr11:65837595-65837645	T-47D	breast:	n/a
27	chr11:65837595-65837645	NHDF-neo	bronchial:	n/a
28	chr11:65837595-65837645	SKMC	muscle:	n/a
29	chr11:65837595-65837645	AoSMC	blood vessel:	n/a
30	chr11:65837595-65837645	Caco-2	colon:	n/a
31	chr11:65837595-65837645	GM06990	blood:	n/a
32	chr11:65837595-65837645	BE2_C	brain:	n/a
33	chr11:65837595-65837645	GM12891	blood:	n/a
34	chr11:65837595-65837645	HEEpiC	esophagus:	n/a
35	chr11:65837595-65837645	NHBE	bronchial:	n/a
36	chr11:65837595-65837645	CMK	blood:	n/a
37	chr11:65837595-65837645	HCF	heart:	n/a
38	chr11:65837595-65837645	HCPEpiC	choroid plexus:	n/a
39	chr11:65837595-65837645	U87	brain:	n/a
40	chr11:65837595-65837645	HRCEpiC	kidney:	n/a
41	chr11:65837595-65837645	AG09309	skin:	n/a
42	chr11:65837595-65837645	NH-A	brain:	n/a
43	chr11:65837595-65837645	HCT-116	colon:	n/a
44	chr11:65837595-65837645	HIPEpiC	eye:	n/a
45	chr11:65837595-65837645	HAEpiC	amniotic membrane:	n/a
46	chr11:65837595-65837645	ECC-1	luminal epithelium:	n/a
47	chr11:65837595-65837645	ovcar-3	ovarian:	n/a
48	chr11:65837595-65837645	PFSK-1	brain:	n/a
49	chr11:65837595-65837645	ProgFib	skin:	n/a
50	chr11:65837595-65837645	Hepatocyte	liver:	n/a

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:65654924..65660442-chr11:65834310..65838665,6	K562	blood:
2	chr11:65816864..65823380-chr11:65832037..65840391,16	MCF-7	breast:
3	chr11:65656719..65659047-chr11:65835301..65837715,2	MCF-7	breast:
4	chr11:65665582..65668888-chr11:65835107..65838015,3	K562	blood:
5	chr11:65836209..65839625-chr11:66023244..66027607,5	K562	blood:
6	chr11:65836630..65840121-chr11:66032259..66035828,5	MCF-7	breast:
7	chr11:65779081..65782393-chr11:65836476..65839425,3	MCF-7	breast:
8	chr11:65837353..65839732-chr11:66024702..66027312,4	MCF-7	breast:
9	chr11:65835858..65838956-chr11:66027814..66030508,4	MCF-7	breast:
10	chr11:65836782..65838328-chr20:49347114..49348947,2	MCF-7	breast:
11	chr11:65836209..65839676-chr11:66023244..66028603,5	K562	blood:
12	chr11:65654924..65661575-chr11:65833688..65838665,10	K562	blood:
13	chr11:65826244..65833224-chr11:65834439..65839387,11	MCF-7	breast:
14	chr11:65685063..65688035-chr11:65836071..65837888,2	MCF-7	breast:
15	chr11:65625072..65626937-chr11:65835477..65837832,2	K562	blood:
16	chr11:65768121..65772581-chr11:65835630..65838620,4	MCF-7	breast:

No data

Variant related genes	Relation type
PACS1	TF binding region
ENSG00000255038	TF binding region
ENSG00000255038	CpG island
PACS1	CpG island
ENSG00000124171	Chromatin interaction
ENSG00000175602	Chromatin interaction
ENSG00000172500	Chromatin interaction
ENSG00000254461	Chromatin interaction
ENSG00000175334	Chromatin interaction
ENSG00000172757	Chromatin interaction
ENSG00000087365	Chromatin interaction
ENSG00000175550	Chromatin interaction
ENSG00000175315	Chromatin interaction
ENSG00000175376	Chromatin interaction
ENSG00000174996	Chromatin interaction
ENSG00000175592	Chromatin interaction
ENSG00000254855	Chromatin interaction
ENSG00000175573	Chromatin interaction
ENSG00000254762	Chromatin interaction
ENSG00000238752	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs11227395	0.84[EUR][1000 genomes]
rs2452681	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948711	chr11:65692760-65949674	Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	65 gene(s)	inside rSNPs	diseases
2	nsv897768	chr11:65715210-65842064	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
3	esv3335923	chr11:65741698-66175759	Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv1819302	chr11:65787660-66007018	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	esv3407551	chr11:65794503-66158322	Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	esv3321690	chr11:65835376-65839974	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Strong transcription Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
7	esv3377128	chr11:65836776-65839324	Flanking Active TSS Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases
8	esv3340048	chr11:65837001-65839549	Active TSS Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:65828200-65838000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:65836200-65837600	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
3	chr11:65836400-65837600	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr11:65836600-65837600	Flanking Active TSS	Primary hematopoietic stem cells	blood
5	chr11:65836600-65837600	Flanking Active TSS	Colonic Mucosa	Colon
6	chr11:65836800-65837600	Flanking Active TSS	Primary B cells from cord blood	blood
7	chr11:65836800-65837600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr11:65836800-65839000	Active TSS	Primary T cells from cord blood	blood
9	chr11:65836800-65839600	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
10	chr11:65837000-65837600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr11:65837000-65837600	Flanking Active TSS	Fetal Brain Female	brain
12	chr11:65837000-65837600	Flanking Active TSS	GM12878-XiMat	blood
13	chr11:65837000-65838400	Transcr. at gene 5' and 3'	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr11:65837000-65838400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr11:65837000-65838800	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr11:65837000-65838800	Active TSS	Brain Substantia Nigra	brain
17	chr11:65837000-65839000	Active TSS	H1 Cell Line	embryonic stem cell
18	chr11:65837000-65839000	Active TSS	HUES64 Cell Line	embryonic stem cell
19	chr11:65837000-65839200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr11:65837000-65839200	Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr11:65837000-65839200	Active TSS	Pancreatic Islets	Pancreatic Islet
22	chr11:65837000-65839400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr11:65837000-65839600	Active TSS	HUES48 Cell Line	embryonic stem cell
24	chr11:65837000-65839800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr11:65837200-65837600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr11:65837200-65837600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr11:65837200-65837600	Enhancers	Fetal Brain Male	brain
28	chr11:65837200-65837600	Active TSS	Stomach Mucosa	stomach
29	chr11:65837200-65837600	Flanking Active TSS	Dnd41	blood
30	chr11:65837200-65837600	Flanking Active TSS	HMEC	breast
31	chr11:65837200-65837800	Weak transcription	NHDF-Ad	bronchial
32	chr11:65837200-65838000	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
33	chr11:65837200-65838000	Weak transcription	Fetal Kidney	kidney
34	chr11:65837200-65838400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr11:65837200-65838600	Active TSS	HUES6 Cell Line	embryonic stem cell
36	chr11:65837200-65838600	Active TSS	iPS-15b Cell Line	embryonic stem cell
37	chr11:65837200-65838600	Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr11:65837200-65838600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
39	chr11:65837200-65838600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr11:65837200-65838600	Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr11:65837200-65838600	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr11:65837200-65838600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr11:65837200-65838600	Active TSS	Brain Angular Gyrus	brain
44	chr11:65837200-65838600	Active TSS	Brain Inferior Temporal Lobe	brain
45	chr11:65837200-65838600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr11:65837200-65838600	Active TSS	Fetal Intestine Small	intestine
47	chr11:65837200-65838600	Active TSS	Fetal Lung	lung
48	chr11:65837200-65838600	Active TSS	Fetal Stomach	stomach
49	chr11:65837200-65838600	Active TSS	Rectal Mucosa Donor 31	rectum
50	chr11:65837200-65838600	Active TSS	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links