Variant report

Variant	rs11964542
Chromosome Location	chr6:30071760-30071761
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:30070774-30071764	H1-hESC	embryonic stem cell:	n/a	n/a
2	CTCF	chr6:30071566-30071784	GM12878	blood:	n/a	n/a
3	CTCF	chr6:30071629-30071760	NHEK	skin:	n/a	n/a
4	CTCF	chr6:30071628-30071789	MCF-7	breast:	n/a	n/a
5	CTCF	chr6:30071640-30071790	GM12864	blood:	n/a	n/a
6	RAD21	chr6:30070507-30071879	SK-N-SH	brain:	n/a	n/a
7	CTCF	chr6:30069267-30071939	SK-N-SH	brain:	n/a	n/a
8	CTCF	chr6:30069586-30072183	A549	lung:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:30070301..30072986-chr6:30097734..30100221,43	MCF-7	breast:
2	chr6:30070449..30072089-chr6:30137197..30138565,6	MCF-7	breast:
3	chr6:30071292..30074099-chr6:30075439..30077084,2	K562	blood:
4	chr6:30039673..30045870-chr6:30065915..30071954,9	MCF-7	breast:
5	chr6:30027872..30030809-chr6:30069511..30072907,4	K562	blood:
6	chr6:30068684..30075353-chr6:30179679..30184952,7	MCF-7	breast:
7	chr6:30070180..30072059-chr6:30098450..30099535,14	K562	blood:
8	chr6:30043377..30045110-chr6:30070275..30072110,2	MCF-7	breast:
9	chr6:30070471..30072023-chr6:30098513..30099477,20	MCF-7	breast:
10	chr6:29944151..29946628-chr6:30070054..30072125,2	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TRIM31-1	chr6:30071650-30071944	NONHSAT108599
2	lnc-TRIM31-1	chr6:30071708-30071944	NONHSAT108600

No data

Variant related genes	Relation type
TRIM31-AS1	TF binding region
ENSG00000234127	Chromatin interaction
ENSG00000066379	Chromatin interaction
ENSG00000204623	Chromatin interaction
ENSG00000204625	Chromatin interaction
ENSG00000204618	Chromatin interaction
ENSG00000204610	Chromatin interaction
ENSG00000204616	Chromatin interaction

Extended variants
information (count: 6 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs17187896	0.93[ASN][1000 genomes]
rs17188050	0.85[ASN][1000 genomes]
rs17194209	0.93[ASN][1000 genomes]
rs6915431	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6915823	0.93[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432866	chr6:30026321-30080921	Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:30068000-30072600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:30068200-30071800	Flanking Active TSS	NHEK	skin
3	chr6:30069000-30071800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:30069400-30071800	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
5	chr6:30069800-30071800	Active TSS	Rectal Smooth Muscle	rectum
6	chr6:30070000-30071800	Enhancers	Spleen	Spleen
7	chr6:30070000-30075400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr6:30070200-30071800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
9	chr6:30070400-30071800	Flanking Active TSS	Duodenum Mucosa	Duodenum
10	chr6:30070800-30072000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr6:30071000-30071800	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
12	chr6:30071000-30071800	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
13	chr6:30071000-30071800	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
14	chr6:30071000-30071800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
15	chr6:30071000-30071800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
16	chr6:30071000-30071800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:30071000-30071800	Flanking Active TSS	Fetal Intestine Small	intestine
18	chr6:30071000-30071800	Active TSS	HSMMtube	muscle
19	chr6:30071200-30071800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
20	chr6:30071200-30071800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr6:30071200-30071800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr6:30071200-30071800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr6:30071200-30071800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr6:30071400-30071800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr6:30071400-30071800	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
26	chr6:30071400-30071800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
27	chr6:30071400-30071800	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
28	chr6:30071400-30071800	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
29	chr6:30071400-30071800	Bivalent/Poised TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:30071400-30071800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
31	chr6:30071400-30071800	Flanking Bivalent TSS/Enh	Brain Substantia Nigra	brain
32	chr6:30071400-30071800	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
33	chr6:30071400-30071800	Bivalent Enhancer	Fetal Stomach	stomach
34	chr6:30071400-30071800	Flanking Active TSS	HepG2	liver
35	chr6:30071400-30071800	Flanking Active TSS	Osteobl	bone
36	chr6:30071400-30073200	Enhancers	Hela-S3	cervix
37	chr6:30071600-30071800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
38	chr6:30071600-30071800	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr6:30071600-30071800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
40	chr6:30071600-30071800	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr6:30071600-30071800	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:30071600-30071800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr6:30071600-30071800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:30071600-30071800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr6:30071600-30071800	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr6:30071600-30071800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
47	chr6:30071600-30071800	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
48	chr6:30071600-30071800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
49	chr6:30071600-30071800	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
50	chr6:30071600-30071800	Active TSS	Primary T helper naive cells from peripheral blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links