Variant report

Variant	rs73400572
Chromosome Location	chr6:28179523-28179524
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28179507..28182174-chr6:28248291..28251754,3	K562	blood:
2	chr6:28167517..28171168-chr6:28177888..28180588,3	K562	blood:
3	chr6:28134260..28137056-chr6:28179298..28181872,3	K562	blood:
4	chr6:28078804..28081627-chr6:28178928..28180967,2	K562	blood:
5	chr6:28122889..28124668-chr6:28176710..28180566,3	K562	blood:
6	chr6:28177601..28182191-chr6:28315411..28319291,5	K562	blood:
7	chr6:28175786..28178014-chr6:28179307..28182825,4	MCF-7	breast:
8	chr6:28128639..28130932-chr6:28178698..28181130,2	K562	blood:
9	chr6:27856295..27859168-chr6:28179121..28180729,2	K562	blood:
10	chr6:28104315..28106178-chr6:28177345..28180593,3	MCF-7	breast:
11	chr6:28179220..28181310-chr6:28303360..28306255,2	MCF-7	breast:
12	chr6:28179297..28181762-chr6:28193422..28195568,2	MCF-7	breast:
13	chr6:28108322..28111152-chr6:28178112..28181694,4	K562	blood:
14	chr6:28178232..28180361-chr6:28366158..28368738,2	K562	blood:
15	chr6:28134260..28137056-chr6:28179298..28182084,4	K562	blood:
16	chr6:28178129..28180295-chr6:28233395..28236371,2	K562	blood:
17	chr6:28103775..28107091-chr6:28177064..28180460,3	K562	blood:
18	chr6:28151155..28153263-chr6:28178363..28180275,2	K562	blood:
19	chr6:28178359..28182415-chr6:28302345..28306363,5	K562	blood:
20	chr6:28103775..28113920-chr6:28177995..28190115,32	K562	blood:
21	chr6:27864015..27866427-chr6:28176005..28180203,3	K562	blood:
22	chr6:28126773..28130386-chr6:28178914..28182864,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000197153	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000269293	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs16893827	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17720687	0.81[ASN][1000 genomes]
rs60913498	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66487884	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs73400575	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73400581	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7757215	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883514	chr6:28155418-28185726	Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv883515	chr6:28156476-28181675	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv883516	chr6:28156476-28185726	Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28178200-28179600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:28178200-28179600	Weak transcription	NHEK	skin
3	chr6:28178400-28180000	Weak transcription	HSMMtube	muscle
4	chr6:28178600-28180000	Weak transcription	Pancreas	Pancrea
5	chr6:28179200-28179600	Bivalent Enhancer	HepG2	liver
6	chr6:28179200-28179600	Flanking Active TSS	K562	blood
7	chr6:28179200-28180200	Bivalent Enhancer	Placenta	Placenta
8	chr6:28179400-28179600	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
9	chr6:28179400-28179600	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
10	chr6:28179400-28179600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
11	chr6:28179400-28179600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr6:28179400-28179600	Enhancers	HMEC	breast
13	chr6:28179400-28180000	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr6:28179400-28180400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
15	chr6:28179400-28180400	Flanking Active TSS	GM12878-XiMat	blood
16	chr6:28179400-28180600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
17	chr6:28179400-28180600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
18	chr6:28179400-28180600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
19	chr6:28179400-28181000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
20	chr6:28179400-28181200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
21	chr6:28179400-28181200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links