Variant report

Variant	rs1146240
Chromosome Location	chr6:109661930-109661931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr6:109661041-109662010	PBDE	blood:	n/a	chr6:109661720-109661729
2	TAL1	chr6:109661416-109661954	K562	blood:	n/a	n/a
3	RCOR1	chr6:109661496-109661967	K562	blood:	n/a	n/a
4	TEAD4	chr6:109661430-109661960	K562	blood:	n/a	n/a
5	MYC	chr6:109661481-109661938	K562	blood:	n/a	n/a
6	TEAD4	chr6:109661338-109662023	K562	blood:	n/a	n/a
7	NR2F2	chr6:109661518-109662108	K562	blood:	n/a	n/a
8	GATA2	chr6:109661442-109661953	K562	blood:	n/a	chr6:109661720-109661729
9	ARID3A	chr6:109661341-109662200	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:109660514..109663248-chr6:109671174..109674117,2	K562	blood:
2	chr6:109655737..109658352-chr6:109659760..109662191,3	K562	blood:
3	chr6:109659415..109661984-chr6:109702237..109705687,4	MCF-7	breast:
4	chr6:109661580..109663132-chr6:109665605..109668214,2	MCF-7	breast:
5	chr6:109656032..109659893-chr6:109659967..109664099,6	MCF-7	breast:
6	chr6:109635700..109637262-chr6:109660535..109662631,2	K562	blood:
7	chr6:109615706..109617299-chr6:109661071..109663820,2	MCF-7	breast:
8	chr6:109571423..109573781-chr6:109659713..109661931,2	MCF-7	breast:
9	chr6:109660483..109663037-chr6:109663413..109665260,2	K562	blood:

No data

Variant related genes	Relation type
CCDC162P	TF binding region
ENSG00000203799	Chromatin interaction
ENSG00000260273	Chromatin interaction
ENSG00000135535	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs6937229	1.00[ASW][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7769789	1.00[ASW][hapmap]

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	nsv5435	chr6:109633035-109669127	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1146240	ZBTB24	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:109644600-109675200	Weak transcription	Primary T cells from cord blood	blood
2	chr6:109645400-109662400	Weak transcription	Aorta	Aorta
3	chr6:109654000-109669400	Weak transcription	Small Intestine	intestine
4	chr6:109654200-109671000	Weak transcription	Spleen	Spleen
5	chr6:109654200-109675000	Weak transcription	Primary B cells from peripheral blood	blood
6	chr6:109654200-109676200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
7	chr6:109654400-109668800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr6:109656800-109662600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr6:109657800-109662200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr6:109657800-109662200	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr6:109657800-109671000	Weak transcription	Lung	lung
12	chr6:109658200-109663600	Weak transcription	Left Ventricle	heart
13	chr6:109658400-109665200	Weak transcription	Fetal Intestine Small	intestine
14	chr6:109658400-109669200	Weak transcription	Liver	Liver
15	chr6:109658600-109662200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr6:109658600-109662200	Weak transcription	Right Ventricle	heart
17	chr6:109658600-109668200	Weak transcription	Colonic Mucosa	Colon
18	chr6:109658600-109670600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr6:109658800-109662000	Weak transcription	Adipose Nuclei	Adipose
20	chr6:109658800-109663600	Weak transcription	Gastric	stomach
21	chr6:109658800-109663600	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr6:109658800-109670600	Weak transcription	Right Atrium	heart
23	chr6:109658800-109677000	Weak transcription	Fetal Stomach	stomach
24	chr6:109660200-109677200	Weak transcription	Thymus	Thymus
25	chr6:109660400-109662000	Enhancers	Rectal Mucosa Donor 31	rectum
26	chr6:109660400-109674600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr6:109660600-109665800	Enhancers	Fetal Muscle Leg	muscle
28	chr6:109660600-109666000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr6:109660800-109666000	Enhancers	Primary hematopoietic stem cells short term culture	blood
30	chr6:109661200-109662400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr6:109661200-109665000	Weak transcription	Pancreas	Pancrea
32	chr6:109661200-109668600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr6:109661400-109662400	Weak transcription	Fetal Muscle Trunk	muscle
34	chr6:109661400-109662600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
35	chr6:109661400-109662800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:109661400-109662800	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr6:109661400-109671400	Weak transcription	Fetal Thymus	thymus
38	chr6:109661600-109662200	Weak transcription	Brain Anterior Caudate	brain
39	chr6:109661600-109663000	Enhancers	HSMMtube	muscle
40	chr6:109661600-109663600	Weak transcription	Primary hematopoietic stem cells	blood
41	chr6:109661600-109663600	Weak transcription	Placenta	Placenta
42	chr6:109661800-109662200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:109661800-109663000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr6:109661800-109663000	Enhancers	K562	blood
45	chr6:109661800-109663600	Weak transcription	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links