Variant report

Variant	rs3130838
Chromosome Location	chr6:28866528-28866529
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	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
2	chr6:28803400..28808440-chr6:28861740..28869149,12	K562	blood:
3	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
4	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
5	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
6	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
7	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:
8	chr6:28864161..28868397-chr6:28882536..28888078,6	MCF-7	breast:
9	chr6:28864176..28867304-chr6:28972657..28975728,3	K562	blood:
10	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000225595	Chromatin interaction
ENSG00000212240	Chromatin interaction
ENSG00000227214	Chromatin interaction
ENSG00000213916	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000204709	Chromatin interaction

Extended variants
information (count: 136 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs1233579	0.80[EUR][1000 genomes]
rs1233580	0.80[EUR][1000 genomes]
rs1233581	0.80[EUR][1000 genomes]
rs1233583	0.80[EUR][1000 genomes]
rs1233593	0.80[EUR][1000 genomes]
rs1233594	0.80[EUR][1000 genomes]
rs1233599	0.84[EUR][1000 genomes]
rs1233600	0.84[EUR][1000 genomes]
rs1233604	0.84[EUR][1000 genomes]
rs1233618	0.84[EUR][1000 genomes]
rs1233620	0.84[EUR][1000 genomes]
rs1233623	0.84[EUR][1000 genomes]
rs1238262	0.80[EUR][1000 genomes]
rs1311912	0.80[EUR][1000 genomes]
rs1311913	0.80[EUR][1000 genomes]
rs13206458	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3117146	0.96[EUR][1000 genomes]
rs3118357	1.00[EUR][1000 genomes]
rs3118359	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3118360	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118361	0.96[EUR][1000 genomes]
rs3118364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3118365	0.94[EUR][1000 genomes]
rs3118366	0.98[EUR][1000 genomes]
rs3118367	1.00[EUR][1000 genomes]
rs3129791	0.89[EUR][1000 genomes]
rs3129794	0.96[EUR][1000 genomes]
rs3129797	0.96[EUR][1000 genomes]
rs3129798	0.96[EUR][1000 genomes]
rs3130837	1.00[EUR][1000 genomes]
rs3130844	0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	0.93[EUR][1000 genomes]
rs3130847	0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.98[EUR][1000 genomes]
rs3130888	0.96[EUR][1000 genomes]
rs3130890	0.85[EUR][1000 genomes]
rs3130891	0.96[EUR][1000 genomes]
rs3130892	0.96[EUR][1000 genomes]
rs3130893	0.96[EUR][1000 genomes]
rs3130894	0.96[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	0.96[EUR][1000 genomes]
rs3131068	0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	0.96[EUR][1000 genomes]
rs3131072	0.96[EUR][1000 genomes]
rs3131073	0.93[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	0.96[EUR][1000 genomes]
rs3131081	0.96[EUR][1000 genomes]
rs3131085	0.92[EUR][1000 genomes]
rs3131093	0.98[EUR][1000 genomes]
rs3131094	1.00[EUR][1000 genomes]
rs3131095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131096	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131101	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131335	0.98[EUR][1000 genomes]
rs3131336	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131340	0.89[EUR][1000 genomes]
rs3131341	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131343	0.87[EUR][1000 genomes]
rs3131345	1.00[EUR][1000 genomes]
rs3132373	0.87[EUR][1000 genomes]
rs3132374	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132376	1.00[EUR][1000 genomes]
rs3132378	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132382	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132384	1.00[EUR][1000 genomes]
rs3132385	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132387	0.98[EUR][1000 genomes]
rs3132388	1.00[EUR][1000 genomes]
rs3132389	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132391	1.00[EUR][1000 genomes]
rs3132392	1.00[EUR][1000 genomes]
rs3132393	0.98[EUR][1000 genomes]
rs3132394	0.98[EUR][1000 genomes]
rs3132395	0.98[EUR][1000 genomes]
rs3132396	0.89[EUR][1000 genomes]
rs3135293	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135294	0.87[EUR][1000 genomes]
rs3135295	1.00[EUR][1000 genomes]
rs3135297	0.94[EUR][1000 genomes]
rs3135298	0.98[EUR][1000 genomes]
rs3135299	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135300	1.00[EUR][1000 genomes]
rs3135302	1.00[EUR][1000 genomes]
rs3135304	1.00[EUR][1000 genomes]
rs3135306	1.00[EUR][1000 genomes]
rs3135307	1.00[EUR][1000 genomes]
rs3135308	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135309	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135311	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135316	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135317	0.96[EUR][1000 genomes]
rs3135318	0.96[EUR][1000 genomes]
rs3135325	0.96[EUR][1000 genomes]
rs4324798	0.89[EUR][1000 genomes]
rs7760313	0.98[EUR][1000 genomes]
rs7761321	0.87[EUR][1000 genomes]
rs7764642	0.82[EUR][1000 genomes]
rs7766699	0.84[EUR][1000 genomes]
rs7767099	0.87[EUR][1000 genomes]
rs9257133	0.80[EUR][1000 genomes]
rs9257136	0.80[EUR][1000 genomes]
rs9257137	0.80[EUR][1000 genomes]
rs9257140	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257167	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9257183	0.84[EUR][1000 genomes]
rs9257184	0.84[EUR][1000 genomes]
rs9257187	0.84[EUR][1000 genomes]
rs9257188	0.84[EUR][1000 genomes]
rs9257189	0.84[EUR][1000 genomes]
rs9257192	0.84[EUR][1000 genomes]
rs9257217	0.87[EUR][1000 genomes]
rs9257223	0.89[EUR][1000 genomes]
rs9257227	0.85[EUR][1000 genomes]
rs9257245	0.98[EUR][1000 genomes]
rs9257249	0.96[EUR][1000 genomes]
rs9257250	0.96[EUR][1000 genomes]
rs9257262	1.00[EUR][1000 genomes]
rs9257267	0.96[EUR][1000 genomes]
rs9257272	1.00[EUR][1000 genomes]
rs9257331	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9257345	1.00[AMR][1000 genomes];0.89[EUR][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	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
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3130838	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3130838	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3130838	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28863000-28866600	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr6:28863000-28867200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:28865000-28868400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr6:28865000-28868400	Weak transcription	Spleen	Spleen
5	chr6:28865000-28868800	Weak transcription	Lung	lung
6	chr6:28865000-28869200	Weak transcription	Gastric	stomach
7	chr6:28865000-28870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr6:28865000-28870600	Weak transcription	Stomach Mucosa	stomach
9	chr6:28865000-28870800	Weak transcription	Small Intestine	intestine
10	chr6:28865200-28868400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr6:28865200-28868800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr6:28865200-28869000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr6:28865200-28869000	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr6:28865200-28869000	Weak transcription	Colonic Mucosa	Colon
15	chr6:28865200-28869200	Weak transcription	Esophagus	oesophagus
16	chr6:28865200-28869200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr6:28865200-28870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr6:28865200-28871400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr6:28865200-28878200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr6:28865400-28867800	Weak transcription	NH-A	brain
21	chr6:28865400-28868400	Weak transcription	Aorta	Aorta
22	chr6:28865400-28868400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr6:28865400-28868400	Weak transcription	Brain Germinal Matrix	brain
24	chr6:28865400-28868400	Weak transcription	Fetal Brain Female	brain
25	chr6:28865400-28868400	Weak transcription	Psoas Muscle	Psoas
26	chr6:28865400-28869000	Weak transcription	Fetal Brain Male	brain
27	chr6:28865400-28869600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:28865400-28870600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
29	chr6:28865400-28870600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr6:28865600-28867000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr6:28865600-28867600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr6:28865600-28867800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:28865600-28867800	Weak transcription	HSMM	muscle
34	chr6:28865600-28868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr6:28865600-28868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr6:28865600-28869000	Weak transcription	Brain Angular Gyrus	brain
37	chr6:28865600-28869000	Weak transcription	Brain Anterior Caudate	brain
38	chr6:28865600-28869000	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr6:28865600-28869000	Weak transcription	HSMMtube	muscle
40	chr6:28865600-28870400	Weak transcription	Brain Substantia Nigra	brain
41	chr6:28865600-28870800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr6:28865600-28871600	Weak transcription	Fetal Heart	heart
43	chr6:28865800-28866600	Active TSS	Hela-S3	cervix
44	chr6:28865800-28866800	Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr6:28865800-28867600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr6:28865800-28867800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr6:28865800-28867800	Weak transcription	HMEC	breast
48	chr6:28865800-28868400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr6:28865800-28868400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr6:28865800-28868400	Weak transcription	GM12878-XiMat	blood

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