Variant report

Variant	rs7775657
Chromosome Location	chr6:28835252-28835253
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr6:28834067-28835259	HepG2	liver:	n/a	n/a
2	MAX	chr6:28834103-28835270	A549	lung:	n/a	n/a
3	POLR2A	chr6:28834079-28835280	H1-neurons	neurons:	n/a	n/a
4	REST	chr6:28834002-28835434	H1-neurons	neurons:	n/a	n/a
5	SIN3AK20	chr6:28834004-28835264	MCF-7	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:28803282..28808663-chr6:28829877..28836776,13	K562	blood:
2	chr6:28835176..28837889-chr6:28857457..28859067,2	K562	blood:
3	chr6:28834360..28837411-chr6:28839003..28841254,4	K562	blood:
4	chr6:28802885..28808466-chr6:28831550..28836351,8	MCF-7	breast:
5	chr6:28833478..28838269-chr6:28843234..28846516,6	MCF-7	breast:
6	chr6:28833109..28835315-chr6:29719168..29721447,2	K562	blood:
7	chr6:28825252..28827430-chr6:28833633..28835942,2	MCF-7	breast:
8	chr6:28833493..28835780-chr6:28880062..28881962,2	MCF-7	breast:
9	chr6:28835058..28836917-chr6:28845496..28848053,2	MCF-7	breast:
10	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
11	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
12	chr6:28833354..28837219-chr6:28837839..28842041,5	MCF-7	breast:
13	chr6:28810165..28812490-chr6:28833681..28835706,2	MCF-7	breast:
14	chr6:28831130..28836886-chr6:28890033..28892870,9	MCF-7	breast:
15	chr6:28833368..28835844-chr6:28972691..28974962,2	MCF-7	breast:
16	chr6:28834738..28837746-chr6:28847549..28850161,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000225595	TF binding region
ENSG00000204713	Chromatin interaction
ENSG00000233366	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000272236	Chromatin interaction
ENSG00000224157	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10428805	0.87[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11756140	1.00[ASN][1000 genomes]
rs11758303	1.00[ASN][1000 genomes]
rs12110866	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58377234	1.00[EUR][1000 genomes]
rs59303422	1.00[ASN][1000 genomes]
rs6456858	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6917227	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6924101	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6925173	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6931486	1.00[EUR][1000 genomes]
rs6934771	1.00[EUR][1000 genomes]
rs6939310	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407222	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407240	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407247	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73407261	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73408940	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7738297	1.00[ASN][1000 genomes]
rs9767253	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534089	chr6:28636972-28841640	Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv883518	chr6:28792477-28911802	Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv883519	chr6:28792477-28936556	Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
4	nsv427748	chr6:28831888-28999434	Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	62 gene(s)	inside rSNPs	diseases
5	nsv601212	chr6:28833225-28893927	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
6	nsv462667	chr6:28834646-28893927	Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7775657	TPBG	trans	lymphoblastoid	seeQTL
rs7775657	CXCL14	trans	lymphoblastoid	seeQTL
rs7775657	ADAM23	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28833400-28835400	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28834800-28835400	Enhancers	Fetal Heart	heart
3	chr6:28835000-28835400	Enhancers	HepG2	liver
4	chr6:28835000-28837000	Enhancers	Fetal Thymus	thymus
5	chr6:28835200-28835400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr6:28835200-28835400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:28835200-28835400	Enhancers	Primary T helper cells PMA-I stimulated	--
8	chr6:28835200-28835400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:28835200-28835400	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr6:28835200-28835400	Active TSS	Fetal Brain Female	brain
11	chr6:28835200-28835600	Enhancers	Fetal Brain Male	brain
12	chr6:28835200-28835600	Enhancers	Fetal Muscle Trunk	muscle
13	chr6:28835200-28835600	Enhancers	Fetal Stomach	stomach
14	chr6:28835200-28835800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr6:28835200-28836000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:28835200-28836200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr6:28835200-28836200	Enhancers	Dnd41	blood
18	chr6:28835200-28836600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr6:28835200-28837000	Enhancers	K562	blood
20	chr6:28835200-28837400	Weak transcription	Thymus	Thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links