Variant report

Variant	rs61896015
Chromosome Location	chr11:47279928-47279929
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:19)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:19 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr11:47279433-47280465	K562	blood:	n/a	n/a
2	CTCF	chr11:47279245-47280031	SK-N-SH	brain:	n/a	n/a
3	CTCF	chr11:47279900-47280050	HVMF	connective:	n/a	n/a
4	CTCF	chr11:47279800-47279950	AG04449	skin:	n/a	n/a
5	RAD21	chr11:47278939-47280017	SK-N-SH	brain:	n/a	n/a
6	MAX	chr11:47279913-47280425	K562	blood:	n/a	n/a
7	POLR2A	chr11:47278875-47279947	HepG2	liver:	n/a	n/a
8	BHLHE40	chr11:47279903-47280304	K562	blood:	n/a	n/a
9	CTCF	chr11:47279820-47279970	HEK293	kidney:	n/a	n/a
10	POLR2A	chr11:47278832-47280214	K562	blood:	n/a	n/a
11	CTCF	chr11:47278588-47281976	A549	lung:	n/a	chr11:47278969-47278982
12	SMARCC1	chr11:47278643-47280119	Hela-S3	cervix:	n/a	n/a
13	SMARCB1	chr11:47278799-47280012	Hela-S3	cervix:	n/a	n/a
14	SMC3	chr11:47279011-47280065	SK-N-SH	brain:	n/a	n/a
15	MAZ	chr11:47278807-47280171	IMR90	lung:	n/a	chr11:47279428-47279438
16	HCFC1	chr11:47278486-47281950	Hela-S3	cervix:	n/a	n/a
17	ZBTB7A	chr11:47279112-47279941	K562	blood:	n/a	n/a
18	CBX3	chr11:47279830-47280335	K562	blood:	n/a	n/a
19	CTCF	chr11:47279417-47280237	K562	blood:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:47197631..47199665-chr11:47279516..47282212,2	K562	blood:
2	chr11:47196892..47202921-chr11:47278417..47285951,9	MCF-7	breast:
3	chr11:47279843..47284326-chr11:47288675..47293634,16	MCF-7	breast:
4	chr11:47265054..47272453-chr11:47272862..47282933,17	MCF-7	breast:
5	chr11:47205592..47209017-chr11:47278399..47281373,5	MCF-7	breast:
6	chr11:47268496..47273681-chr11:47277782..47283365,10	K562	blood:
7	chr11:47277979..47283267-chr11:47289057..47293509,9	K562	blood:
8	chr11:47267134..47271941-chr11:47277592..47282899,11	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MADD-2	chr11:47279547-47280057	NONHSAT021221

No data

Variant related genes	Relation type
NR1H3	TF binding region
ENSG00000165912	Chromatin interaction
ENSG00000134575	Chromatin interaction
ENSG00000110514	Chromatin interaction
ENSG00000149182	Chromatin interaction
ENSG00000025434	Chromatin interaction
ENSG00000256746	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10838694	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11039157	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11530168	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12221497	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12573962	0.93[AMR][1000 genomes]
rs12575157	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12575296	0.83[AMR][1000 genomes]
rs12576461	0.83[AMR][1000 genomes]
rs12576690	0.83[AMR][1000 genomes]
rs12576751	0.86[AMR][1000 genomes]
rs12577319	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17726390	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3736101	0.83[AMR][1000 genomes]
rs3758668	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758671	0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3758674	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3816724	0.86[AMR][1000 genomes]
rs41301449	0.93[AMR][1000 genomes]
rs41304347	0.86[AMR][1000 genomes]
rs41310332	0.86[AMR][1000 genomes]
rs45489595	0.90[AMR][1000 genomes]
rs55764401	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56168519	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56177220	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56825896	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56886689	1.00[AFR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61896047	0.93[AMR][1000 genomes]
rs61896051	0.86[AMR][1000 genomes]
rs61896053	0.83[AMR][1000 genomes]
rs61896054	0.83[AMR][1000 genomes]
rs61897361	0.83[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv897323	chr11:47182926-47460306	Genic enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv917316	chr11:47232210-47448882	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs61896015	PACSIN3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47271000-47280800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr11:47271400-47281000	Weak transcription	Thymus	Thymus
3	chr11:47271400-47281200	Weak transcription	Primary B cells from peripheral blood	blood
4	chr11:47271400-47281200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr11:47271400-47281200	Weak transcription	Primary T helper cells fromperipheralblood	blood
6	chr11:47271400-47281200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:47272400-47286400	Weak transcription	Dnd41	blood
8	chr11:47275800-47286800	Weak transcription	Primary T cells from cord blood	blood
9	chr11:47276800-47280800	Weak transcription	HSMMtube	muscle
10	chr11:47277000-47282000	Weak transcription	Spleen	Spleen
11	chr11:47278600-47280000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr11:47278600-47280200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
13	chr11:47278600-47280200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr11:47278600-47280400	Enhancers	Small Intestine	intestine
15	chr11:47278600-47281600	Enhancers	Fetal Heart	heart
16	chr11:47278600-47282000	Flanking Active TSS	Hela-S3	cervix
17	chr11:47278800-47280000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
18	chr11:47278800-47280000	Flanking Active TSS	A549	lung
19	chr11:47278800-47280000	Enhancers	HUVEC	blood vessel
20	chr11:47278800-47280200	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr11:47278800-47280200	Flanking Active TSS	Colonic Mucosa	Colon
22	chr11:47278800-47280200	Flanking Active TSS	Fetal Muscle Trunk	muscle
23	chr11:47278800-47280200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
24	chr11:47278800-47280200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr11:47278800-47281000	Flanking Active TSS	Stomach Smooth Muscle	stomach
26	chr11:47278800-47281600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr11:47278800-47281600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr11:47278800-47282000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr11:47278800-47282200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr11:47278800-47282200	Flanking Active TSS	Adipose Nuclei	Adipose
31	chr11:47279000-47280000	Active TSS	ES-I3 Cell Line	embryonic stem cell
32	chr11:47279000-47280000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr11:47279000-47280000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr11:47279000-47280000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr11:47279000-47280000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
36	chr11:47279000-47280000	Flanking Active TSS	Fetal Muscle Leg	muscle
37	chr11:47279000-47280000	Flanking Active TSS	HSMM	muscle
38	chr11:47279000-47280200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
39	chr11:47279000-47280200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr11:47279000-47280200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
41	chr11:47279000-47280200	Flanking Active TSS	Placenta	Placenta
42	chr11:47279000-47280200	Flanking Active TSS	Left Ventricle	heart
43	chr11:47279000-47280200	Flanking Active TSS	K562	blood
44	chr11:47279000-47280200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
45	chr11:47279000-47280400	Flanking Active TSS	Colon Smooth Muscle	Colon
46	chr11:47279000-47280400	Flanking Active TSS	Fetal Stomach	stomach
47	chr11:47279000-47280400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr11:47279000-47281600	Enhancers	Placenta Amnion	Placenta Amnion
49	chr11:47279000-47281600	Enhancers	NH-A	brain
50	chr11:47279200-47280000	Active TSS	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links