Variant report

Variant	rs3135293
Chromosome Location	chr6:28877247-28877248
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28877196-28878162	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr6:28877092-28877889	SK-N-MC	brain:	n/a	n/a
3	POLR2A	chr6:28877033-28879022	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr6:28877201-28877721	HepG2	liver:	n/a	n/a
5	POLR2A	chr6:28877136-28879784	K562	blood:	n/a	n/a
6	POLR2A	chr6:28877092-28878032	HepG2	liver:	n/a	n/a
7	POLR2A	chr6:28877153-28877748	K562	blood:	n/a	n/a
8	POLR2A	chr6:28877154-28877849	PFSK-1	brain:	n/a	n/a
9	POLR2A	chr6:28877163-28879808	K562	blood:	n/a	n/a
10	POLR2A	chr6:28876413-28878953	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28874958..28881784-chr6:28883001..28892669,21	MCF-7	breast:
2	chr6:28874441..28877573-chr6:28886876..28891614,6	MCF-7	breast:

Variant related genes	Relation type
TRIM27	TF binding region
ENSG00000204713	Chromatin interaction
ENSG00000212240	Chromatin interaction

Extended variants
information (count: 137 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:131)

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]
rs3130777	1.00[AFR][1000 genomes];0.82[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]
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]
rs3135316	1.00[AFR][1000 genomes];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
rs3135293	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs3135293	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs3135293	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	chr6:28865200-28878200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:28866000-28887000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr6:28867000-28889400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr6:28867600-28889200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr6:28867600-28889400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr6:28867600-28889600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:28867800-28878800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr6:28867800-28880000	Strong transcription	Primary T cells from cord blood	blood
9	chr6:28867800-28881600	Strong transcription	HSMM	muscle
10	chr6:28867800-28883200	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr6:28867800-28885400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr6:28867800-28888200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr6:28867800-28888400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr6:28867800-28888400	Strong transcription	Fetal Thymus	thymus
15	chr6:28867800-28889200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
16	chr6:28867800-28889200	Strong transcription	HMEC	breast
17	chr6:28867800-28889400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr6:28867800-28889400	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr6:28867800-28889600	Strong transcription	Fetal Lung	lung
20	chr6:28868000-28878400	Strong transcription	Placenta	Placenta
21	chr6:28868000-28889200	Strong transcription	HUES6 Cell Line	embryonic stem cell
22	chr6:28868200-28880200	Strong transcription	Primary hematopoietic stem cells	blood
23	chr6:28868200-28887200	Strong transcription	HUVEC	blood vessel
24	chr6:28868200-28889600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr6:28868200-28889800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:28868400-28878400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
27	chr6:28868400-28878400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr6:28868400-28878600	Strong transcription	NHEK	skin
29	chr6:28868400-28879600	Strong transcription	Brain Cingulate Gyrus	brain
30	chr6:28868400-28879800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
31	chr6:28868400-28879800	Strong transcription	GM12878-XiMat	blood
32	chr6:28868400-28880200	Strong transcription	Thymus	Thymus
33	chr6:28868400-28880600	Strong transcription	Brain Germinal Matrix	brain
34	chr6:28868400-28881000	Strong transcription	Cortex derived primary cultured neurospheres	brain
35	chr6:28868400-28881000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr6:28868400-28881600	Strong transcription	Stomach Smooth Muscle	stomach
37	chr6:28868400-28882600	Strong transcription	Liver	Liver
38	chr6:28868400-28884400	Strong transcription	Dnd41	blood
39	chr6:28868400-28886800	Strong transcription	Primary T cells fromperipheralblood	blood
40	chr6:28868400-28887200	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr6:28868400-28888400	Strong transcription	Adipose Nuclei	Adipose
42	chr6:28868400-28888400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr6:28868400-28888400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
44	chr6:28868400-28888400	Strong transcription	Fetal Brain Female	brain
45	chr6:28868400-28888400	Strong transcription	Fetal Muscle Leg	muscle
46	chr6:28868400-28888600	Strong transcription	Fetal Muscle Trunk	muscle
47	chr6:28868400-28889000	Strong transcription	Sigmoid Colon	Sigmoid Colon
48	chr6:28868400-28889200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr6:28868400-28889400	Strong transcription	H1 Cell Line	embryonic stem cell
50	chr6:28868400-28889400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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