Variant report

Variant	rs3132378
Chromosome Location	chr6:28885865-28885866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28864161..28868397-chr6:28882536..28888078,6	MCF-7	breast:
2	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:
3	chr6:28869658..28871297-chr6:28885676..28887250,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000224157	Chromatin interaction
ENSG00000204713	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:98)

rs_ID	r²[population]
rs13206458	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3117146	0.89[EUR][1000 genomes]
rs3118357	0.92[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3118364	1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3118365	0.87[EUR][1000 genomes]
rs3118366	0.90[EUR][1000 genomes]
rs3118367	0.92[EUR][1000 genomes]
rs3129791	1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130777	1.00[AFR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3130838	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3130844	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130845	0.96[EUR][1000 genomes]
rs3130846	1.00[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs3130847	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130885	0.94[EUR][1000 genomes]
rs3130887	0.91[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3131068	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131069	0.96[EUR][1000 genomes]
rs3131071	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131072	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131073	0.93[EUR][1000 genomes]
rs3131075	0.96[EUR][1000 genomes]
rs3131076	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3131081	0.89[EUR][1000 genomes]
rs3131085	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3131093	0.91[EUR][1000 genomes]
rs3131094	0.92[EUR][1000 genomes]
rs3131095	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131096	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131097	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131101	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131335	0.90[EUR][1000 genomes]
rs3131336	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3131340	0.81[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3131345	0.92[EUR][1000 genomes]
rs3132374	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132376	0.92[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132384	0.92[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132387	0.91[EUR][1000 genomes]
rs3132388	0.92[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132391	0.92[EUR][1000 genomes]
rs3132392	0.92[EUR][1000 genomes]
rs3132393	0.90[EUR][1000 genomes]
rs3132394	0.90[EUR][1000 genomes]
rs3132395	0.90[EUR][1000 genomes]
rs3132396	0.81[EUR][1000 genomes]
rs3135293	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135295	0.92[EUR][1000 genomes]
rs3135297	0.94[EUR][1000 genomes]
rs3135298	0.90[EUR][1000 genomes]
rs3135299	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3135300	0.92[EUR][1000 genomes]
rs3135302	0.92[EUR][1000 genomes]
rs3135304	0.92[EUR][1000 genomes]
rs3135306	0.92[EUR][1000 genomes]
rs3135307	0.92[EUR][1000 genomes]
rs3135308	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135309	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135310	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135311	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135312	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135313	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135316	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3135318	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3135325	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs4324798	0.81[EUR][1000 genomes]
rs7760313	0.91[EUR][1000 genomes]
rs9257140	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9257167	0.87[AMR][1000 genomes]
rs9257223	0.81[EUR][1000 genomes]
rs9257245	0.91[EUR][1000 genomes]
rs9257249	0.96[EUR][1000 genomes]
rs9257250	0.96[EUR][1000 genomes]
rs9257262	0.92[EUR][1000 genomes]
rs9257267	0.89[EUR][1000 genomes]
rs9257272	0.92[EUR][1000 genomes]
rs9257331	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9257345	1.00[AMR][1000 genomes];0.96[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
rs3132378	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3132378	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3132378	ZFP57	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr6:28867000-28889400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:28867600-28889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr6:28867600-28889400	Strong transcription	HUES48 Cell Line	embryonic stem cell
5	chr6:28867600-28889600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:28867800-28888200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr6:28867800-28888400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr6:28867800-28888400	Strong transcription	Fetal Thymus	thymus
9	chr6:28867800-28889200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr6:28867800-28889200	Strong transcription	HMEC	breast
11	chr6:28867800-28889400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr6:28867800-28889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr6:28867800-28889600	Strong transcription	Fetal Lung	lung
14	chr6:28868000-28889200	Strong transcription	HUES6 Cell Line	embryonic stem cell
15	chr6:28868200-28887200	Strong transcription	HUVEC	blood vessel
16	chr6:28868200-28889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
17	chr6:28868200-28889800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
18	chr6:28868400-28886800	Strong transcription	Primary T cells fromperipheralblood	blood
19	chr6:28868400-28887200	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr6:28868400-28888400	Strong transcription	Adipose Nuclei	Adipose
21	chr6:28868400-28888400	Strong transcription	Duodenum Mucosa	Duodenum
22	chr6:28868400-28888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr6:28868400-28888400	Strong transcription	Fetal Brain Female	brain
24	chr6:28868400-28888400	Strong transcription	Fetal Muscle Leg	muscle
25	chr6:28868400-28888600	Strong transcription	Fetal Muscle Trunk	muscle
26	chr6:28868400-28889000	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr6:28868400-28889200	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr6:28868400-28889400	Strong transcription	H1 Cell Line	embryonic stem cell
29	chr6:28868400-28889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr6:28868600-28887200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr6:28868600-28887800	Strong transcription	Left Ventricle	heart
32	chr6:28868600-28888400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr6:28868600-28888600	Strong transcription	Duodenum Smooth Muscle	Duodenum
34	chr6:28868600-28889400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr6:28868600-28889400	Strong transcription	Fetal Intestine Large	intestine
36	chr6:28868600-28889800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr6:28868800-28887200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr6:28869000-28888600	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:28869000-28889400	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr6:28869200-28886800	Strong transcription	Primary B cells from peripheral blood	blood
41	chr6:28869600-28889200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:28869600-28889600	Strong transcription	Fetal Stomach	stomach
43	chr6:28870200-28889000	Strong transcription	Fetal Intestine Small	intestine
44	chr6:28870600-28887400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
45	chr6:28871800-28887200	Strong transcription	K562	blood
46	chr6:28872000-28887600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr6:28872600-28886800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr6:28875000-28887200	Weak transcription	Stomach Mucosa	stomach
49	chr6:28875400-28887400	Weak transcription	Fetal Heart	heart
50	chr6:28875800-28889400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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