Variant report

Variant	rs3131341
Chromosome Location	chr6:28778723-28778724
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28774872..28779186-chr6:28780865..28786550,9	K562	blood:
2	chr6:28778307..28780155-chr6:28804697..28807128,2	K562	blood:
3	chr6:28692413..28694711-chr6:28778373..28780345,2	K562	blood:
4	chr6:28687938..28689790-chr6:28777726..28779382,2	K562	blood:
5	chr6:28771451..28773263-chr6:28777101..28779175,2	K562	blood:
6	chr6:28777118..28779341-chr6:28889220..28890745,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204713	Chromatin interaction
ENSG00000225173	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs1233579	0.84[EUR][1000 genomes]
rs1233580	0.84[EUR][1000 genomes]
rs1233581	0.84[EUR][1000 genomes]
rs1233583	0.84[EUR][1000 genomes]
rs1233593	0.84[EUR][1000 genomes]
rs1233594	0.84[EUR][1000 genomes]
rs1233599	0.87[EUR][1000 genomes]
rs1233600	0.87[EUR][1000 genomes]
rs1233604	0.87[EUR][1000 genomes]
rs1233618	0.87[EUR][1000 genomes]
rs1233620	0.87[EUR][1000 genomes]
rs1233623	0.87[EUR][1000 genomes]
rs1238262	0.84[EUR][1000 genomes]
rs1311911	0.82[EUR][1000 genomes]
rs1311912	0.84[EUR][1000 genomes]
rs1311913	0.84[EUR][1000 genomes]
rs13194504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs13206458	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13217472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1742743	0.82[EUR][1000 genomes]
rs3118357	0.89[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3118364	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3118365	0.84[EUR][1000 genomes]
rs3118366	0.87[EUR][1000 genomes]
rs3118367	0.89[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130838	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130845	0.85[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130885	0.83[EUR][1000 genomes]
rs3130887	0.87[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130895	0.84[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131069	0.85[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131073	0.82[EUR][1000 genomes]
rs3131075	0.85[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131093	0.87[EUR][1000 genomes]
rs3131094	0.89[EUR][1000 genomes]
rs3131095	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131096	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131097	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131101	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3131335	0.87[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131340	1.00[EUR][1000 genomes]
rs3131343	0.98[EUR][1000 genomes]
rs3131345	0.89[EUR][1000 genomes]
rs3132373	0.98[EUR][1000 genomes]
rs3132374	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132376	0.89[EUR][1000 genomes]
rs3132378	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3132384	0.89[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132387	0.87[EUR][1000 genomes]
rs3132388	0.89[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132391	0.89[EUR][1000 genomes]
rs3132392	0.89[EUR][1000 genomes]
rs3132393	0.87[EUR][1000 genomes]
rs3132394	0.87[EUR][1000 genomes]
rs3132395	0.87[EUR][1000 genomes]
rs3132396	1.00[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135294	0.98[EUR][1000 genomes]
rs3135295	0.89[EUR][1000 genomes]
rs3135297	0.83[EUR][1000 genomes]
rs3135298	0.87[EUR][1000 genomes]
rs3135299	1.00[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3135300	0.89[EUR][1000 genomes]
rs3135302	0.89[EUR][1000 genomes]
rs3135304	0.89[EUR][1000 genomes]
rs3135306	0.89[EUR][1000 genomes]
rs3135307	0.89[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135309	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135310	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135311	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135312	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135313	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs34724414	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35044849	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35243068	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4324798	1.00[EUR][1000 genomes]
rs7760313	0.87[EUR][1000 genomes]
rs7761321	0.98[EUR][1000 genomes]
rs7764642	0.85[EUR][1000 genomes]
rs7766699	0.95[EUR][1000 genomes]
rs7767099	0.98[EUR][1000 genomes]
rs9257133	0.84[EUR][1000 genomes]
rs9257136	0.84[EUR][1000 genomes]
rs9257137	0.84[EUR][1000 genomes]
rs9257140	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9257167	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9257183	0.87[EUR][1000 genomes]
rs9257184	0.87[EUR][1000 genomes]
rs9257187	0.87[EUR][1000 genomes]
rs9257188	0.87[EUR][1000 genomes]
rs9257189	0.87[EUR][1000 genomes]
rs9257192	0.87[EUR][1000 genomes]
rs9257217	0.98[EUR][1000 genomes]
rs9257223	1.00[EUR][1000 genomes]
rs9257227	0.96[EUR][1000 genomes]
rs9257245	0.87[EUR][1000 genomes]
rs9257249	0.85[EUR][1000 genomes]
rs9257250	0.85[EUR][1000 genomes]
rs9257262	0.89[EUR][1000 genomes]
rs9257267	0.85[EUR][1000 genomes]
rs9257272	0.89[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9257345	0.87[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv883517	chr6:28751727-28802149	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2621756	chr6:28762692-28779791	Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	esv2322180	chr6:28764675-28780578	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	esv9558	chr6:28770281-28785058	Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	esv3410540	chr6:28770455-28785112	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	esv3322630	chr6:28770519-28785092	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv3486939	chr6:28770525-28785051	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	esv3486940	chr6:28770525-28785051	Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
10	esv3403106	chr6:28770790-28785189	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	nsv970724	chr6:28778144-28784760	Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3131341	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3131341	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3131341	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28776800-28779200	Weak transcription	Hela-S3	cervix
2	chr6:28777000-28779000	Active TSS	A549	lung
3	chr6:28777600-28778800	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
4	chr6:28777600-28778800	Bivalent Enhancer	Fetal Muscle Leg	muscle
5	chr6:28777600-28779400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr6:28777800-28778800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
7	chr6:28777800-28778800	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr6:28777800-28778800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr6:28777800-28778800	Flanking Bivalent TSS/Enh	HepG2	liver
10	chr6:28777800-28778800	Bivalent/Poised TSS	HSMMtube	muscle
11	chr6:28777800-28778800	Flanking Bivalent TSS/Enh	NHEK	skin
12	chr6:28777800-28778800	Flanking Bivalent TSS/Enh	Osteobl	bone
13	chr6:28777800-28779000	Flanking Active TSS	HMEC	breast
14	chr6:28778000-28778800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
15	chr6:28778000-28778800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
16	chr6:28778000-28778800	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:28778000-28778800	Bivalent Enhancer	Brain Cingulate Gyrus	brain
18	chr6:28778000-28778800	Bivalent Enhancer	Esophagus	oesophagus
19	chr6:28778000-28778800	Enhancers	Pancreas	Pancrea
20	chr6:28778000-28779800	Flanking Active TSS	K562	blood
21	chr6:28778200-28778800	Bivalent Enhancer	Fetal Stomach	stomach
22	chr6:28778200-28778800	ZNF genes & repeats	Right Atrium	heart
23	chr6:28778200-28778800	Bivalent/Poised TSS	GM12878-XiMat	blood
24	chr6:28778200-28781600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr6:28778400-28778800	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr6:28778400-28778800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr6:28778400-28778800	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr6:28778400-28778800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
29	chr6:28778400-28778800	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr6:28778400-28778800	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
31	chr6:28778400-28778800	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr6:28778400-28778800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
33	chr6:28778400-28778800	Bivalent Enhancer	Placenta	Placenta
34	chr6:28778400-28778800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
35	chr6:28778400-28778800	Bivalent Enhancer	HUVEC	blood vessel
36	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
37	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	H9 Cell Line	embryonic stem cell
40	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr6:28778600-28778800	Bivalent Enhancer	Brain Hippocampus Middle	brain
49	chr6:28778600-28778800	Bivalent Enhancer	Fetal Lung	lung
50	chr6:28778600-28778800	Flanking Bivalent TSS/Enh	HSMM	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links