Variant report

Variant	rs3135316
Chromosome Location	chr6:28864849-28864850
allele	A/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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28761882..28764605-chr6:28861705..28864953,3	K562	blood:
2	chr13:111521903..111522810-chr6:28864546..28865505,2	Hela-S3	cervix:
3	chr6:28830882..28836292-chr6:28860588..28866545,10	MCF-7	breast:
4	chr6:28803400..28808440-chr6:28861740..28869149,12	K562	blood:
5	chr6:28828478..28839935-chr6:28855092..28866386,31	K562	blood:
6	chr6:28861427..28866893-chr6:28947878..28954176,14	K562	blood:
7	chr6:28864761..28865369-chr6:44216136..44216861,2	Hela-S3	cervix:
8	chr2:20646523..20647378-chr6:28864213..28864977,2	Hela-S3	cervix:
9	chr6:28859278..28869415-chr6:28906395..28912460,18	K562	blood:
10	chr6:28861427..28869364-chr6:28946251..28954176,23	K562	blood:
11	chr6:28861677..28871493-chr6:28888734..28892704,20	MCF-7	breast:
12	chr6:28823126..28835109-chr6:28859268..28867076,23	K562	blood:
13	chr6:28864161..28868397-chr6:28882536..28888078,6	MCF-7	breast:
14	chr1:165796618..165797277-chr6:28864608..28865190,2	Hela-S3	cervix:
15	chr6:28864176..28867304-chr6:28972657..28975728,3	K562	blood:
16	chr6:28861810..28871966-chr6:28889574..28894668,20	MCF-7	breast:
17	chr6:28802724..28808694-chr6:28856997..28865691,21	K562	blood:

No data

Variant related genes	Relation type
ENSG00000143878	Chromatin interaction
ENSG00000143179	Chromatin interaction
ENSG00000265764	Chromatin interaction
ENSG00000204709	Chromatin interaction
ENSG00000212240	Chromatin interaction
ENSG00000143183	Chromatin interaction
ENSG00000197935	Chromatin interaction
ENSG00000225173	Chromatin interaction
ENSG00000204713	Chromatin interaction
ENSG00000225595	Chromatin interaction
ENSG00000213916	Chromatin interaction
ENSG00000255874	Chromatin interaction
ENSG00000227214	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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3117146	0.96[EUR][1000 genomes]
rs3118357	1.00[EUR][1000 genomes]
rs3118359	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3118360	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3118361	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3118364	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	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs3129794	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129797	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3129798	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130837	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3130838	1.00[AMR][1000 genomes];1.00[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	0.98[EUR][1000 genomes]
rs3130888	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130890	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs3130891	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130892	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130893	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130894	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs3130895	0.94[EUR][1000 genomes]
rs3130896	1.00[AFR][1000 genomes];0.96[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	0.96[EUR][1000 genomes]
rs3131085	1.00[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3131093	0.98[EUR][1000 genomes]
rs3131094	1.00[EUR][1000 genomes]
rs3131095	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131096	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131097	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	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3131340	0.89[EUR][1000 genomes]
rs3131341	1.00[AFR][1000 genomes];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[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3132382	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3132384	1.00[EUR][1000 genomes]
rs3132385	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3132387	0.98[EUR][1000 genomes]
rs3132388	1.00[EUR][1000 genomes]
rs3132389	1.00[AFR][1000 genomes];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[AFR][1000 genomes];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	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[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135309	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135310	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135311	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135312	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135313	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3135317	1.00[AFR][1000 genomes];0.96[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	0.89[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	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9257167	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[AFR][1000 genomes];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
rs3135316	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3135316	ZFP57	Cis_1M	lymphoblastoid	RTeQTL
rs3135316	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	chr6:28862800-28865200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr6:28862800-28865200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr6:28862800-28865200	Active TSS	Duodenum Smooth Muscle	Duodenum
4	chr6:28862800-28865400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr6:28862800-28866000	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr6:28862800-28866200	Active TSS	Fetal Stomach	stomach
7	chr6:28862800-28866200	Active TSS	Rectal Mucosa Donor 29	rectum
8	chr6:28862800-28866400	Active TSS	HUES64 Cell Line	embryonic stem cell
9	chr6:28862800-28866400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:28862800-28866400	Active TSS	Fetal Lung	lung
11	chr6:28863000-28865000	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
12	chr6:28863000-28865000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr6:28863000-28865000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
14	chr6:28863000-28865000	Active TSS	Brain Anterior Caudate	brain
15	chr6:28863000-28865000	Active TSS	Stomach Mucosa	stomach
16	chr6:28863000-28865200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr6:28863000-28865200	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr6:28863000-28865200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
19	chr6:28863000-28865200	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr6:28863000-28865200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr6:28863000-28865200	Active TSS	Adipose Nuclei	Adipose
22	chr6:28863000-28865200	Active TSS	Brain Inferior Temporal Lobe	brain
23	chr6:28863000-28865200	Active TSS	Colonic Mucosa	Colon
24	chr6:28863000-28865200	Active TSS	Colon Smooth Muscle	Colon
25	chr6:28863000-28865200	Active TSS	Duodenum Mucosa	Duodenum
26	chr6:28863000-28865200	Active TSS	Fetal Heart	heart
27	chr6:28863000-28865200	Active TSS	Fetal Intestine Large	intestine
28	chr6:28863000-28865200	Active TSS	Placenta Amnion	Placenta Amnion
29	chr6:28863000-28865200	Active TSS	Rectal Smooth Muscle	rectum
30	chr6:28863000-28865200	Active TSS	Skeletal Muscle Male	skeletal muscle
31	chr6:28863000-28865200	Active TSS	Thymus	Thymus
32	chr6:28863000-28865200	Active TSS	GM12878-XiMat	blood
33	chr6:28863000-28865200	Active TSS	NH-A	brain
34	chr6:28863000-28865400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr6:28863000-28865400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr6:28863000-28865400	Active TSS	Aorta	Aorta
37	chr6:28863000-28865400	Active TSS	Brain Angular Gyrus	brain
38	chr6:28863000-28865400	Active TSS	Brain Cingulate Gyrus	brain
39	chr6:28863000-28865400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:28863000-28865400	Active TSS	Psoas Muscle	Psoas
41	chr6:28863000-28865400	Active TSS	Hela-S3	cervix
42	chr6:28863000-28865400	Active TSS	HSMM	muscle
43	chr6:28863000-28865600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr6:28863000-28865600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr6:28863000-28865600	Active TSS	Brain Substantia Nigra	brain
46	chr6:28863000-28865600	Active TSS	Skeletal Muscle Female	skeletal muscle
47	chr6:28863000-28865600	Active TSS	HSMMtube	muscle
48	chr6:28863000-28865800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr6:28863000-28865800	Active TSS	Fetal Muscle Trunk	muscle
50	chr6:28863000-28865800	Active TSS	HMEC	breast

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