Variant report

Variant	rs3130890
Chromosome Location	chr6:28957139-28957140
allele	C/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr6:28914281..28916611-chr6:28956056..28957643,2	K562	blood:
2	chr6:28926035..28928870-chr6:28956157..28957921,2	K562	blood:
3	chr6:28915108..28916611-chr6:28956143..28957725,2	K562	blood:
4	chr6:28955433..28959890-chr6:28970874..28974365,4	MCF-7	breast:
5	chr6:28805954..28808293-chr6:28955372..28957939,3	K562	blood:
6	chr6:28956755..28959002-chr6:28959086..28960670,2	MCF-7	breast:
7	chr6:28955940..28958074-chr6:28964364..28967031,2	MCF-7	breast:
8	chr6:28956424..28958160-chr6:28982849..28984604,2	K562	blood:
9	chr6:26156919..26159659-chr6:28956488..28958543,2	MCF-7	breast:
10	chr6:28956538..28957176-chr6:28984206..28985119,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000197935	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 104 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs13206458	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3117146	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3118357	0.85[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3118364	0.81[EUR][1000 genomes]
rs3118365	0.80[EUR][1000 genomes]
rs3118366	0.84[EUR][1000 genomes]
rs3118367	0.85[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130777	1.00[AFR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3130838	0.85[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3130845	0.82[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3130885	0.80[EUR][1000 genomes]
rs3130887	0.84[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130895	0.80[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3131069	0.82[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3131075	0.82[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3131081	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131085	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131093	0.84[EUR][1000 genomes]
rs3131094	0.85[EUR][1000 genomes]
rs3131095	0.85[EUR][1000 genomes]
rs3131096	0.85[EUR][1000 genomes]
rs3131097	0.85[EUR][1000 genomes]
rs3131335	0.84[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes]
rs3131345	0.85[EUR][1000 genomes]
rs3132374	0.82[EUR][1000 genomes]
rs3132376	0.85[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3132384	0.85[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3132387	0.84[EUR][1000 genomes]
rs3132388	0.85[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3132391	0.85[EUR][1000 genomes]
rs3132392	0.85[EUR][1000 genomes]
rs3132393	0.84[EUR][1000 genomes]
rs3132394	0.84[EUR][1000 genomes]
rs3132395	0.84[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3135295	0.85[EUR][1000 genomes]
rs3135297	0.80[EUR][1000 genomes]
rs3135298	0.84[EUR][1000 genomes]
rs3135299	0.82[EUR][1000 genomes]
rs3135300	0.85[EUR][1000 genomes]
rs3135302	0.85[EUR][1000 genomes]
rs3135304	0.85[EUR][1000 genomes]
rs3135306	0.85[EUR][1000 genomes]
rs3135307	0.85[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3135309	0.85[EUR][1000 genomes]
rs3135310	0.85[EUR][1000 genomes]
rs3135311	0.85[EUR][1000 genomes]
rs3135312	0.85[EUR][1000 genomes]
rs3135313	0.85[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7760313	0.84[EUR][1000 genomes]
rs9257245	0.84[EUR][1000 genomes]
rs9257249	0.82[EUR][1000 genomes]
rs9257250	0.82[EUR][1000 genomes]
rs9257262	0.85[EUR][1000 genomes]
rs9257267	0.82[EUR][1000 genomes]
rs9257272	0.85[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv830622	chr6:28861667-29015804	Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
3	nsv1023540	chr6:28922691-29326018	Active TSS Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv538169	chr6:28922691-29326018	Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
5	nsv869541	chr6:28922692-29326017	Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
6	nsv916439	chr6:28922697-29326087	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
7	nsv462668	chr6:28922719-29342775	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
8	nsv601213	chr6:28922719-29342775	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
9	nsv1015796	chr6:28923980-29342825	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
10	nsv462669	chr6:28936556-29337500	Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
11	nsv601214	chr6:28936556-29337500	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
12	nsv601215	chr6:28946920-29348297	ZNF genes & repeats Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	45 gene(s)	inside rSNPs	diseases
13	nsv1023028	chr6:28956136-29343575	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
14	nsv538170	chr6:28956136-29343575	ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
15	nsv1018937	chr6:28956136-29366175	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3130890	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3130890	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3130890	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28955800-28957200	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28955800-28957200	Active TSS	H1 Cell Line	embryonic stem cell
3	chr6:28955800-28957200	Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr6:28955800-28957200	Active TSS	HUES64 Cell Line	embryonic stem cell
5	chr6:28955800-28957200	Active TSS	iPS-18 Cell Line	embryonic stem cell
6	chr6:28956000-28957200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:28956000-28957200	Active TSS	HUES6 Cell Line	embryonic stem cell
8	chr6:28956000-28957200	Active TSS	iPS-15b Cell Line	embryonic stem cell
9	chr6:28956000-28957200	Active TSS	iPS-20b Cell Line	embryonic stem cell
10	chr6:28956000-28957200	Active TSS	K562	blood
11	chr6:28956400-28957200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr6:28956600-28963200	Weak transcription	Pancreas	Pancrea
13	chr6:28956800-28957200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr6:28956800-28957200	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr6:28956800-28962800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr6:28956800-28963200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr6:28957000-28957200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr6:28957000-28957200	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
19	chr6:28957000-28957200	Enhancers	Placenta	Placenta
20	chr6:28957000-28958000	Weak transcription	HepG2	liver
21	chr6:28957000-28963000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr6:28957000-28963000	Weak transcription	Brain Anterior Caudate	brain

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