Variant report

Variant	rs3132374
Chromosome Location	chr6:28868494-28868495
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28803400..28808440-chr6:28861740..28869149,12	K562	blood:
2	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
3	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
4	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
5	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204709	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000227214	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1233599	0.80[EUR][1000 genomes]
rs1233600	0.80[EUR][1000 genomes]
rs1233604	0.80[EUR][1000 genomes]
rs1233618	0.80[EUR][1000 genomes]
rs1233620	0.80[EUR][1000 genomes]
rs1233623	0.80[EUR][1000 genomes]
rs13206458	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3117146	0.93[EUR][1000 genomes]
rs3118357	0.96[EUR][1000 genomes]
rs3118359	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3118360	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3118361	0.93[EUR][1000 genomes]
rs3118364	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3118365	0.91[EUR][1000 genomes]
rs3118366	0.94[EUR][1000 genomes]
rs3118367	0.96[EUR][1000 genomes]
rs3129791	0.85[EUR][1000 genomes]
rs3129794	0.93[EUR][1000 genomes]
rs3129797	0.93[EUR][1000 genomes]
rs3129798	0.93[EUR][1000 genomes]
rs3130837	0.96[EUR][1000 genomes]
rs3130838	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3130844	0.93[EUR][1000 genomes]
rs3130845	0.93[EUR][1000 genomes]
rs3130846	0.89[EUR][1000 genomes]
rs3130847	0.93[EUR][1000 genomes]
rs3130885	0.91[EUR][1000 genomes]
rs3130887	0.94[EUR][1000 genomes]
rs3130888	0.93[EUR][1000 genomes]
rs3130890	0.82[EUR][1000 genomes]
rs3130891	0.93[EUR][1000 genomes]
rs3130892	0.93[EUR][1000 genomes]
rs3130893	0.93[EUR][1000 genomes]
rs3130894	0.93[EUR][1000 genomes]
rs3130895	0.91[EUR][1000 genomes]
rs3130896	0.93[EUR][1000 genomes]
rs3131068	0.93[EUR][1000 genomes]
rs3131069	0.93[EUR][1000 genomes]
rs3131071	0.93[EUR][1000 genomes]
rs3131072	0.93[EUR][1000 genomes]
rs3131073	0.89[EUR][1000 genomes]
rs3131075	0.93[EUR][1000 genomes]
rs3131076	0.93[EUR][1000 genomes]
rs3131081	0.93[EUR][1000 genomes]
rs3131085	0.89[EUR][1000 genomes]
rs3131093	0.94[EUR][1000 genomes]
rs3131094	0.96[EUR][1000 genomes]
rs3131095	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131096	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131097	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131101	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3131335	0.94[EUR][1000 genomes]
rs3131336	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3131340	0.85[EUR][1000 genomes]
rs3131341	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3131343	0.84[EUR][1000 genomes]
rs3131345	0.96[EUR][1000 genomes]
rs3132373	0.84[EUR][1000 genomes]
rs3132376	0.96[EUR][1000 genomes]
rs3132378	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3132382	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3132384	0.96[EUR][1000 genomes]
rs3132385	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132387	0.94[EUR][1000 genomes]
rs3132388	0.96[EUR][1000 genomes]
rs3132389	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132391	0.96[EUR][1000 genomes]
rs3132392	0.96[EUR][1000 genomes]
rs3132393	0.94[EUR][1000 genomes]
rs3132394	0.94[EUR][1000 genomes]
rs3132395	0.94[EUR][1000 genomes]
rs3132396	0.85[EUR][1000 genomes]
rs3135293	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135294	0.84[EUR][1000 genomes]
rs3135295	0.96[EUR][1000 genomes]
rs3135297	0.91[EUR][1000 genomes]
rs3135298	0.94[EUR][1000 genomes]
rs3135299	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3135300	0.96[EUR][1000 genomes]
rs3135302	0.96[EUR][1000 genomes]
rs3135304	0.96[EUR][1000 genomes]
rs3135306	0.96[EUR][1000 genomes]
rs3135307	0.96[EUR][1000 genomes]
rs3135308	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135309	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135310	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135311	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135312	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135313	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135316	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3135317	0.93[EUR][1000 genomes]
rs3135318	0.93[EUR][1000 genomes]
rs3135325	0.93[EUR][1000 genomes]
rs4324798	0.85[EUR][1000 genomes]
rs7760313	0.94[EUR][1000 genomes]
rs7761321	0.84[EUR][1000 genomes]
rs7766699	0.81[EUR][1000 genomes]
rs7767099	0.84[EUR][1000 genomes]
rs9257140	0.87[AMR][1000 genomes]
rs9257167	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257183	0.80[EUR][1000 genomes]
rs9257184	0.80[EUR][1000 genomes]
rs9257187	0.80[EUR][1000 genomes]
rs9257188	0.80[EUR][1000 genomes]
rs9257189	0.80[EUR][1000 genomes]
rs9257192	0.80[EUR][1000 genomes]
rs9257217	0.84[EUR][1000 genomes]
rs9257223	0.85[EUR][1000 genomes]
rs9257227	0.82[EUR][1000 genomes]
rs9257245	0.94[EUR][1000 genomes]
rs9257249	0.93[EUR][1000 genomes]
rs9257250	0.93[EUR][1000 genomes]
rs9257262	0.96[EUR][1000 genomes]
rs9257267	0.93[EUR][1000 genomes]
rs9257272	0.96[EUR][1000 genomes]
rs9257331	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9257345	1.00[AMR][1000 genomes];0.85[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
rs3132374	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3132374	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3132374	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28865000-28868800	Weak transcription	Lung	lung
2	chr6:28865000-28869200	Weak transcription	Gastric	stomach
3	chr6:28865000-28870600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr6:28865000-28870600	Weak transcription	Stomach Mucosa	stomach
5	chr6:28865000-28870800	Weak transcription	Small Intestine	intestine
6	chr6:28865200-28868800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr6:28865200-28869000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr6:28865200-28869000	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr6:28865200-28869000	Weak transcription	Colonic Mucosa	Colon
10	chr6:28865200-28869200	Weak transcription	Esophagus	oesophagus
11	chr6:28865200-28869200	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr6:28865200-28870600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:28865200-28871400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr6:28865200-28878200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr6:28865400-28869000	Weak transcription	Fetal Brain Male	brain
16	chr6:28865400-28869600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr6:28865400-28870600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr6:28865400-28870600	Weak transcription	Rectal Smooth Muscle	rectum
19	chr6:28865600-28868600	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr6:28865600-28868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr6:28865600-28869000	Weak transcription	Brain Angular Gyrus	brain
22	chr6:28865600-28869000	Weak transcription	Brain Anterior Caudate	brain
23	chr6:28865600-28869000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr6:28865600-28869000	Weak transcription	HSMMtube	muscle
25	chr6:28865600-28870400	Weak transcription	Brain Substantia Nigra	brain
26	chr6:28865600-28870800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr6:28865600-28871600	Weak transcription	Fetal Heart	heart
28	chr6:28865800-28868600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:28865800-28868600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
30	chr6:28865800-28868800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
31	chr6:28865800-28869000	Weak transcription	HepG2	liver
32	chr6:28865800-28869200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr6:28866000-28869400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr6:28866000-28870400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr6:28866000-28870400	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:28866000-28870600	Weak transcription	Right Ventricle	heart
37	chr6:28866000-28870800	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:28866000-28871600	Weak transcription	Pancreatic Islets	Pancreatic Islet
39	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
40	chr6:28866200-28868600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:28866200-28868600	Weak transcription	Fetal Intestine Large	intestine
42	chr6:28866200-28868600	Weak transcription	Fetal Kidney	kidney
43	chr6:28866200-28868600	Weak transcription	Left Ventricle	heart
44	chr6:28866200-28869000	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr6:28866200-28869400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:28866200-28869400	Weak transcription	Ovary	ovary
47	chr6:28866200-28869600	Weak transcription	Fetal Stomach	stomach
48	chr6:28866200-28870200	Weak transcription	Fetal Intestine Small	intestine
49	chr6:28866200-28870600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr6:28866200-28874200	Weak transcription	Right Atrium	heart

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