Variant report

Variant	rs6438086
Chromosome Location	chr3:112359986-112359987
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:197)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:197 , 50 per page) page: 1 2 3 4

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:112359734-112360334	K562	blood:	n/a	n/a
2	MAX	chr3:112358983-112360732	A549	lung:	n/a	chr3:112360464-112360473
3	POLR2A	chr3:112358726-112360545	SK-N-SH	brain:	n/a	n/a
4	RCOR1	chr3:112359872-112360245	K562	blood:	n/a	n/a
5	MAX	chr3:112358802-112360786	SK-N-SH	brain:	n/a	chr3:112360464-112360473
6	CEBPB	chr3:112358594-112360673	A549	lung:	n/a	chr3:112358750-112358761
7	POLR2A	chr3:112359738-112360225	A549	lung:	n/a	n/a
8	PBX3	chr3:112359710-112360326	SK-N-SH	brain:	n/a	n/a
9	PML	chr3:112359745-112360341	MCF-7	breast:	n/a	n/a
10	CTCF	chr3:112359722-112360097	K562	blood:	n/a	n/a
11	SIX5	chr3:112359766-112360577	A549	lung:	n/a	n/a
12	POLR2A	chr3:112359741-112360280	HCT-116	colon:	n/a	n/a
13	USF1	chr3:112359835-112360277	A549	lung:	n/a	n/a
14	POLR2A	chr3:112359596-112360338	K562	blood:	n/a	n/a
15	TCF12	chr3:112359737-112360287	A549	lung:	n/a	n/a
16	MAFK	chr3:112358924-112360416	Hela-S3	cervix:	n/a	chr3:112359917-112359932
17	MXI1	chr3:112359494-112360160	K562	blood:	n/a	n/a
18	POLR2A	chr3:112359825-112360166	A549	lung:	n/a	n/a
19	SP1	chr3:112358971-112360621	A549	lung:	n/a	chr3:112359997-112360007
20	MYC	chr3:112359916-112360147	K562	blood:	n/a	n/a
21	MAX	chr3:112359946-112360146	H1-hESC	embryonic stem cell:	n/a	n/a
22	GATA3	chr3:112358736-112360473	SK-N-SH	brain:	n/a	n/a
23	POLR2A	chr3:112359738-112360281	GM12892	blood:	n/a	n/a
24	GATA3	chr3:112359598-112360297	SK-N-SH	brain:	n/a	n/a
25	FOS	chr3:112359868-112360443	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr3:112359860-112360010	HCM	heart:	n/a	n/a
27	POLR2A	chr3:112359588-112360334	K562	blood:	n/a	n/a
28	POLR2A	chr3:112359830-112360201	A549	lung:	n/a	n/a
29	CTCF	chr3:112359900-112360050	HPAF	blood vessel:	n/a	n/a
30	TAF7	chr3:112359712-112360311	K562	blood:	n/a	n/a
31	SMC3	chr3:112359043-112360546	Hela-S3	cervix:	n/a	n/a
32	HCFC1	chr3:112359906-112360209	K562	blood:	n/a	n/a
33	ZBTB33	chr3:112359658-112360390	SK-N-SH	brain:	n/a	n/a
34	POLR2A	chr3:112359526-112360366	K562	blood:	n/a	n/a
35	JUND	chr3:112359855-112360355	H1-hESC	embryonic stem cell:	n/a	n/a
36	STAT3	chr3:112359868-112360182	MCF10A-Er-Src	breast:	n/a	n/a
37	POLR2A	chr3:112359590-112360239	K562	blood:	n/a	n/a
38	RFX5	chr3:112359075-112360492	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr3:112359734-112360198	GM12892	blood:	n/a	n/a
40	REST	chr3:112359772-112360149	SK-N-SH	brain:	n/a	n/a
41	POLR2A	chr3:112358884-112362166	IMR90	lung:	n/a	n/a
42	POLR2A	chr3:112359690-112360293	GM12878	blood:	n/a	n/a
43	POLR2A	chr3:112358922-112360408	MCF10A-Er-Src	breast:	n/a	n/a
44	POLR2A	chr3:112359762-112360285	HUVEC	blood vessel:	n/a	n/a
45	KAP1	chr3:112359019-112360794	HEK293	kidney:	n/a	n/a
46	POLR2A	chr3:112359675-112360278	GM12891	blood:	n/a	n/a
47	SP1	chr3:112359679-112360385	H1-hESC	embryonic stem cell:	n/a	chr3:112359997-112360007
48	POLR2A	chr3:112359801-112360275	HCT-116	colon:	n/a	n/a
49	BCLAF1	chr3:112359748-112360359	K562	blood:	n/a	n/a
50	POLR2A	chr3:112359641-112360383	HCT-116	colon:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:112359885..112361404-chr3:112367931..112369710,2	MCF-7	breast:
2	chr3:112358576..112361067-chr3:112520655..112523598,3	MCF-7	breast:
3	chr3:112289268..112293035-chr3:112358216..112361029,3	MCF-7	breast:
4	chr3:112359858..112360411-chr7:100025644..100026612,2	Hela-S3	cervix:
5	chr3:112358478..112360877-chr3:112708365..112711089,3	MCF-7	breast:
6	chr3:112358855..112360949-chr3:112737036..112738900,2	K562	blood:
7	chr3:112354638..112357493-chr3:112357624..112362114,5	K562	blood:
8	chr3:112358680..112360592-chr3:112737016..112739347,2	MCF-7	breast:
9	chr3:112357856..112364091-chr3:112692717..112699765,9	MCF-7	breast:
10	chr3:112278745..112284115-chr3:112357887..112361363,11	MCF-7	breast:
11	chr3:112358506..112363260-chr3:112706755..112711649,8	K562	blood:
12	chr3:112279172..112282504-chr3:112358640..112361542,6	MCF-7	breast:
13	chr3:112358697..112360499-chr3:112735766..112739410,3	MCF-7	breast:
14	chr3:112279230..112282432-chr3:112358112..112361671,5	K562	blood:
15	chr3:112359721..112360525-chr9:125675165..125676110,2	Hela-S3	cervix:
16	chr17:48784635..48785585-chr3:112359690..112360504,2	Hela-S3	cervix:
17	chr19:19030312..19031078-chr3:112359710..112360246,2	Hela-S3	cervix:
18	chr3:112359608..112361417-chr3:113001269..113003641,2	MCF-7	breast:
19	chr3:112011328..112014210-chr3:112359098..112361496,2	MCF-7	breast:
20	chr3:112357488..112363507-chr3:112707947..112711649,7	K562	blood:
21	chr3:112279230..112281440-chr3:112358030..112362501,6	K562	blood:
22	chr3:112358718..112361602-chr3:112709202..112711684,5	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC80-1	chr3:112359771-112359990	NONHSAT091190

No data

Variant related genes	Relation type
CCDC80	TF binding region
ENSG00000163608	Chromatin interaction
ENSG00000091986	Chromatin interaction
ENSG00000138459	Chromatin interaction
ENSG00000078487	Chromatin interaction
ENSG00000186130	Chromatin interaction
ENSG00000154945	Chromatin interaction
ENSG00000163606	Chromatin interaction
ENSG00000172139	Chromatin interaction
ENSG00000163607	Chromatin interaction
ENSG00000105671	Chromatin interaction
ENSG00000144848	Chromatin interaction
ENSG00000272844	Chromatin interaction
ENSG00000144857	Chromatin interaction
ENSG00000146834	Chromatin interaction
ENSG00000242770	Chromatin interaction
ENSG00000240057	Chromatin interaction

Extended variants
information (count: 11 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs2279531	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6438087	0.91[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6772337	0.90[CEU][hapmap]
rs6794305	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6807798	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7611898	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9683135	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs9815819	0.95[CEU][hapmap];0.89[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9821338	0.89[CHB][hapmap];0.84[CHD][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs9870933	0.91[TSI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329419	chr3:112236688-112620544	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6438086	BOC	cis	cerebellum	SCAN
rs6438086	ESAM	trans	parietal	SCAN

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112354000-112360600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:112354800-112360000	Active TSS	Rectal Mucosa Donor 29	rectum
3	chr3:112355800-112360200	Active TSS	Rectal Mucosa Donor 31	rectum
4	chr3:112356000-112360600	Active TSS	Duodenum Smooth Muscle	Duodenum
5	chr3:112356200-112360000	Active TSS	Brain Substantia Nigra	brain
6	chr3:112357200-112360400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr3:112357200-112361000	Flanking Active TSS	Adipose Nuclei	Adipose
8	chr3:112358000-112360400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:112358000-112360400	Active TSS	Right Ventricle	heart
10	chr3:112358400-112360400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr3:112358600-112360000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:112358600-112360000	Active TSS	Fetal Intestine Large	intestine
13	chr3:112358600-112360000	Active TSS	Placenta Amnion	Placenta Amnion
14	chr3:112358600-112360000	Active TSS	HSMMtube	muscle
15	chr3:112358600-112360200	Active TSS	Brain Hippocampus Middle	brain
16	chr3:112358600-112360200	Active TSS	Colon Smooth Muscle	Colon
17	chr3:112358600-112360400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:112358600-112360400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr3:112358600-112360400	ZNF genes & repeats	Fetal Brain Male	brain
20	chr3:112358600-112360400	Active TSS	HSMM	muscle
21	chr3:112358600-112360600	Flanking Active TSS	HUVEC	blood vessel
22	chr3:112358600-112361800	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr3:112358600-112363200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:112358600-112365400	Weak transcription	Lung	lung
25	chr3:112358800-112360000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:112358800-112360000	Active TSS	Muscle Satellite Cultured Cells	--
27	chr3:112358800-112360000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:112358800-112360000	Active TSS	Fetal Muscle Trunk	muscle
29	chr3:112358800-112360000	Active TSS	Osteobl	bone
30	chr3:112358800-112360200	Active TSS	Fetal Stomach	stomach
31	chr3:112358800-112360200	Active TSS	NHLF	lung
32	chr3:112358800-112360400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr3:112358800-112360400	Active TSS	Ovary	ovary
34	chr3:112358800-112360400	Active TSS	Right Atrium	heart
35	chr3:112358800-112360400	Active TSS	NHDF-Ad	bronchial
36	chr3:112358800-112363200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr3:112359000-112360000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:112359000-112360000	Active TSS	NH-A	brain
39	chr3:112359000-112360200	Active TSS	Aorta	Aorta
40	chr3:112359000-112360200	Active TSS	Skeletal Muscle Female	skeletal muscle
41	chr3:112359000-112360400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr3:112359000-112360400	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr3:112359000-112360400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr3:112359000-112360400	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr3:112359000-112361200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr3:112359000-112363600	Enhancers	iPS-15b Cell Line	embryonic stem cell
47	chr3:112359200-112360000	Active TSS	Brain Angular Gyrus	brain
48	chr3:112359200-112360000	Active TSS	Psoas Muscle	Psoas
49	chr3:112359200-112360200	Active TSS	Fetal Lung	lung
50	chr3:112359200-112360200	Active TSS	A549	lung

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