Variant report

Variant	rs6915678
Chromosome Location	chr6:27235866-27235867
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:183)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	HMGN3	chr6:27235723-27235943	K562	blood:	n/a	n/a
2	CTCF	chr6:27235720-27235870	HBMEC	blood vessel:	n/a	n/a

(count:183 , 50 per page) page: 1 2 3 4

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr6:27235820-27235870	HL-60	blood:	n/a
2	chr6:27235843-27235893	HEEpiC	esophagus:	n/a
3	chr6:27235820-27235870	LNCaP	prostate:	n/a
4	chr6:27235843-27235893	HL-60	blood:	n/a
5	chr6:27235820-27235870	ovcar-3	ovarian:	n/a
6	chr6:27235820-27235870	MCF-7	breast:	n/a
7	chr6:27235843-27235893	SK-N-MC	brain:	n/a
8	chr6:27235822-27235872	NHBE	bronchial:	n/a
9	chr6:27235822-27235872	HCPEpiC	choroid plexus:	n/a
10	chr6:27235822-27235872	SK-N-SH_RA	brain:	n/a
11	chr6:27235820-27235870	ProgFib	skin:	n/a
12	chr6:27235822-27235872	HEEpiC	esophagus:	n/a
13	chr6:27235843-27235893	HepG2	liver:	n/a
14	chr6:27235822-27235872	A549	lung:	n/a
15	chr6:27235820-27235870	GM12892	blood:	n/a
16	chr6:27235822-27235872	HIPEpiC	eye:	n/a
17	chr6:27235843-27235893	HIPEpiC	eye:	n/a
18	chr6:27235822-27235872	RPTEC	kidney:	n/a
19	chr6:27235843-27235893	SKMC	muscle:	n/a
20	chr6:27235820-27235870	GM06990	blood:	n/a
21	chr6:27235820-27235870	Hepatocyte	liver:	n/a
22	chr6:27235843-27235893	HAEpiC	amniotic membrane:	n/a
23	chr6:27235843-27235893	HCT-116	colon:	n/a
24	chr6:27235822-27235872	GM12878	blood:	n/a
25	chr6:27235843-27235893	BJ	skin:	n/a
26	chr6:27235822-27235872	BE2_C	brain:	n/a
27	chr6:27235843-27235893	ECC-1	luminal epithelium:	n/a
28	chr6:27235822-27235872	Caco-2	colon:	n/a
29	chr6:27235822-27235872	GM06990	blood:	n/a
30	chr6:27235820-27235870	PrEC	prostate:	n/a
31	chr6:27235820-27235870	NB4	blood:	n/a
32	chr6:27235822-27235872	GM19239	blood:	n/a
33	chr6:27235820-27235870	ECC-1	luminal epithelium:	n/a
34	chr6:27235822-27235872	GM12891	blood:	n/a
35	chr6:27235843-27235893	K562	blood:	n/a
36	chr6:27235820-27235870	HPAEpiC	pulmonary alveolar:	n/a
37	chr6:27235843-27235893	GM12878	blood:	n/a
38	chr6:27235820-27235870	U87	brain:	n/a
39	chr6:27235843-27235893	RPTEC	kidney:	n/a
40	chr6:27235820-27235870	NHDF-neo	bronchial:	n/a
41	chr6:27235843-27235893	NHDF-neo	bronchial:	n/a
42	chr6:27235822-27235872	NHDF-neo	bronchial:	n/a
43	chr6:27235822-27235872	AG09309	skin:	n/a
44	chr6:27235820-27235870	HRE	kidney:	n/a
45	chr6:27235843-27235893	CMK	blood:	n/a
46	chr6:27235822-27235872	T-47D	breast:	n/a
47	chr6:27235843-27235893	HRCEpiC	kidney:	n/a
48	chr6:27235822-27235872	GM12892	blood:	n/a
49	chr6:27235820-27235870	MCF10A-Er-Src	breast:	n/a
50	chr6:27235843-27235893	MCF10A-Er-Src	breast:	n/a

No data

Variant related genes	Relation type
ENSG00000270935	TF binding region
ENSG00000270935	CpG island

Extended variants
information (count: 20 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs3800316	0.89[LWK][hapmap]
rs6456771	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6902012	0.82[JPT][hapmap]
rs6917419	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs6938397	0.82[JPT][hapmap]
rs7759694	0.96[CEU][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs858986	0.89[CHB][hapmap]
rs9348759	0.82[JPT][hapmap]
rs9366690	0.82[JPT][hapmap]
rs9368500	0.82[JPT][hapmap]
rs9379958	0.82[CEU][hapmap]
rs9379970	0.82[JPT][hapmap]
rs9393795	0.87[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9393796	0.81[CHD][hapmap];0.82[JPT][hapmap]
rs9393801	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9393802	0.82[JPT][hapmap]
rs9393803	0.82[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948921	chr6:26556890-27443957	Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Enhancers Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	472 gene(s)	inside rSNPs	diseases
2	nsv1017328	chr6:27177147-27369588	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv883505	chr6:27210614-27300580	Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs6915678	BTN3A3	cis	cerebellum	SCAN
rs6915678	HIST1H2BH	cis	cerebellum	SCAN
rs6915678	ZSCAN23	cis	parietal	SCAN
rs6915678	HIST1H3D	cis	parietal	SCAN
rs6915678	ZSCAN23	cis	cerebellum	SCAN
rs6915678	BTN3A3	cis	parietal	SCAN
rs6915678	HIST1H2BM	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27232000-27236400	Weak transcription	K562	blood
2	chr6:27235600-27236000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
3	chr6:27235600-27236000	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr6:27235600-27236000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr6:27235600-27236400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
6	chr6:27235800-27236000	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
7	chr6:27235800-27236000	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr6:27235800-27236000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
9	chr6:27235800-27236000	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
10	chr6:27235800-27236000	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr6:27235800-27236000	Bivalent/Poised TSS	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr6:27235800-27236000	Bivalent Enhancer	Esophagus	oesophagus
13	chr6:27235800-27236000	Bivalent Enhancer	Fetal Heart	heart
14	chr6:27235800-27236000	Bivalent Enhancer	Fetal Lung	lung
15	chr6:27235800-27236000	Bivalent Enhancer	Left Ventricle	heart
16	chr6:27235800-27236000	Enhancers	HMEC	breast
17	chr6:27235800-27236000	Flanking Bivalent TSS/Enh	NHEK	skin
18	chr6:27235800-27236200	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr6:27235800-27236200	Active TSS	H9 Cell Line	embryonic stem cell
20	chr6:27235800-27236200	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr6:27235800-27236200	Flanking Bivalent TSS/Enh	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr6:27235800-27236200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
23	chr6:27235800-27236200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
24	chr6:27235800-27236200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
25	chr6:27235800-27236200	Bivalent/Poised TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr6:27235800-27236200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:27235800-27236200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr6:27235800-27236200	Bivalent Enhancer	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr6:27235800-27236200	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:27235800-27236200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:27235800-27236400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell

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