Variant report

Variant	rs9257189
Chromosome Location	chr6:28757555-28757556
allele	C/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28692257..28693945-chr6:28757387..28759135,2	K562	blood:
2	chr6:28677491..28679930-chr6:28756497..28758578,2	K562	blood:
3	chr6:28739775..28742884-chr6:28756307..28759477,3	K562	blood:
4	chr6:28752766..28756379-chr6:28756550..28759154,4	K562	blood:
5	chr6:28755863..28758470-chr6:28911484..28913225,2	K562	blood:
6	chr6:28756425..28760621-chr6:28761088..28764506,5	K562	blood:
7	chr6:28746864..28751693-chr6:28754692..28757727,4	K562	blood:
8	chr6:28665488..28667691-chr6:28756212..28758692,2	K562	blood:
9	chr6:28756573..28759569-chr6:28769791..28772080,4	K562	blood:
10	chr6:28695047..28697144-chr6:28756622..28759292,2	K562	blood:
11	chr6:28757312..28759023-chr6:28889870..28891731,2	K562	blood:
12	chr6:28755863..28759570-chr6:28911484..28914475,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000265764	Chromatin interaction

Extended variants
information (count: 119 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:117)

rs_ID	r²[population]
rs1233579	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233580	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233581	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233583	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233593	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233594	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1233599	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233600	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233604	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233618	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233620	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1233623	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1238262	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1311911	0.94[EUR][1000 genomes]
rs1311912	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1311913	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13194504	0.84[EUR][1000 genomes]
rs13206458	0.80[EUR][1000 genomes]
rs13217472	0.89[EUR][1000 genomes]
rs1742743	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3118357	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3118359	0.84[EUR][1000 genomes]
rs3118360	0.84[EUR][1000 genomes]
rs3118361	0.80[EUR][1000 genomes]
rs3118365	0.86[AFR][1000 genomes]
rs3118366	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3118367	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3130838	0.84[EUR][1000 genomes]
rs3130844	0.80[EUR][1000 genomes]
rs3130845	0.80[EUR][1000 genomes]
rs3130847	0.80[EUR][1000 genomes]
rs3130892	0.80[EUR][1000 genomes]
rs3131068	0.80[EUR][1000 genomes]
rs3131069	0.80[EUR][1000 genomes]
rs3131071	0.80[EUR][1000 genomes]
rs3131072	0.80[EUR][1000 genomes]
rs3131075	0.80[EUR][1000 genomes]
rs3131076	0.80[EUR][1000 genomes]
rs3131093	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3131094	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3131095	0.84[EUR][1000 genomes]
rs3131096	0.84[EUR][1000 genomes]
rs3131097	0.84[EUR][1000 genomes]
rs3131335	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3131336	0.84[EUR][1000 genomes]
rs3131340	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3131341	0.87[EUR][1000 genomes]
rs3131343	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131345	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3132373	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3132374	0.80[EUR][1000 genomes]
rs3132376	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3132382	0.80[EUR][1000 genomes]
rs3132384	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3132385	0.84[EUR][1000 genomes]
rs3132387	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3132388	0.84[EUR][1000 genomes]
rs3132389	0.84[EUR][1000 genomes]
rs3132391	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3132392	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3132393	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3132394	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3132395	0.88[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3132396	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs3135293	0.84[EUR][1000 genomes]
rs3135294	0.85[EUR][1000 genomes]
rs3135295	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3135297	0.84[AFR][1000 genomes]
rs3135298	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs3135300	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3135302	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3135304	0.86[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3135306	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3135307	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs3135308	0.84[EUR][1000 genomes]
rs3135309	0.84[EUR][1000 genomes]
rs3135310	0.84[EUR][1000 genomes]
rs3135311	0.84[EUR][1000 genomes]
rs3135312	0.84[EUR][1000 genomes]
rs3135313	0.84[EUR][1000 genomes]
rs3135316	0.84[EUR][1000 genomes]
rs3135318	0.80[EUR][1000 genomes]
rs3135325	0.80[EUR][1000 genomes]
rs34724414	0.84[EUR][1000 genomes]
rs35044849	0.84[EUR][1000 genomes]
rs35243068	0.89[EUR][1000 genomes]
rs4324798	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs6456835	0.91[EUR][1000 genomes]
rs6908726	0.87[EUR][1000 genomes]
rs6928657	0.83[AFR][1000 genomes]
rs7745088	0.86[AFR][1000 genomes]
rs7760313	0.84[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs7761321	0.93[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7764642	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7766699	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7767099	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9257133	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257136	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257137	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257140	0.96[EUR][1000 genomes]
rs9257167	1.00[EUR][1000 genomes]
rs9257183	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257184	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257187	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257192	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257217	0.88[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9257223	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs9257227	0.84[EUR][1000 genomes]
rs9257245	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs9257250	0.88[AFR][1000 genomes]
rs9257262	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257267	0.86[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9257272	0.88[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9257331	0.84[EUR][1000 genomes]
rs9393926	0.87[EUR][1000 genomes]
rs9393929	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9257189	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs9257189	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs9257189	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28755800-28757600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:28756400-28758600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
3	chr6:28756400-28759200	Active TSS	A549	lung
4	chr6:28756600-28757600	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
5	chr6:28756600-28757600	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
6	chr6:28756600-28757600	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
7	chr6:28756600-28757800	Bivalent/Poised TSS	Primary T cells from cord blood	blood
8	chr6:28756600-28757800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr6:28756600-28758600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:28756600-28759000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
11	chr6:28756800-28757600	Bivalent/Poised TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr6:28756800-28758800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr6:28756800-28759000	Active TSS	Placenta	Placenta
14	chr6:28756800-28759000	Active TSS	K562	blood
15	chr6:28756800-28759200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
16	chr6:28757000-28758200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr6:28757000-28758400	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr6:28757000-28758400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr6:28757000-28758400	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
20	chr6:28757200-28757600	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:28757200-28757600	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr6:28757200-28757600	Bivalent/Poised TSS	Primary T killer memory cells from peripheral blood	blood
23	chr6:28757200-28757600	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr6:28757200-28757600	Flanking Active TSS	Hela-S3	cervix
25	chr6:28757200-28757800	Bivalent Enhancer	Brain Germinal Matrix	brain
26	chr6:28757200-28757800	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
27	chr6:28757200-28757800	Bivalent Enhancer	Fetal Heart	heart
28	chr6:28757200-28758000	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
29	chr6:28757200-28758200	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr6:28757200-28758200	Bivalent/Poised TSS	Fetal Brain Female	brain
31	chr6:28757200-28758200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
32	chr6:28757200-28758200	Bivalent/Poised TSS	Fetal Kidney	kidney
33	chr6:28757200-28758400	Bivalent/Poised TSS	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:28757200-28758400	Bivalent/Poised TSS	Primary hematopoietic stem cells short term culture	blood
35	chr6:28757200-28758400	Bivalent/Poised TSS	Fetal Intestine Large	intestine
36	chr6:28757200-28758600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr6:28757200-28758800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr6:28757200-28759000	Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr6:28757400-28757600	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr6:28757400-28757600	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:28757400-28757600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr6:28757400-28757600	Bivalent Enhancer	Primary B cells from peripheral blood	blood
43	chr6:28757400-28757600	Bivalent Enhancer	Primary hematopoietic stem cells	blood
44	chr6:28757400-28757600	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
45	chr6:28757400-28757600	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
46	chr6:28757400-28757600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
47	chr6:28757400-28757600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
48	chr6:28757400-28757600	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
49	chr6:28757400-28757600	Bivalent/Poised TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr6:28757400-28757600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin

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