Variant report

Variant	rs3825586
Chromosome Location	chr14:24767767-24767768
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
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	CREB1	chr14:24767655-24770253	HepG2	liver:	n/a	n/a
2	MBD4	chr14:24767734-24769920	HepG2	liver:	n/a	n/a

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24701050..24707093-chr14:24765824..24771703,7	K562	blood:
2	chr14:24680927..24686311-chr14:24766466..24771455,6	K562	blood:
3	chr14:24682270..24687913-chr14:24764870..24771791,12	MCF-7	breast:
4	chr14:24614927..24617454-chr14:24767400..24769438,2	K562	blood:
5	chr14:24613977..24617454-chr14:24767400..24769438,3	K562	blood:
6	chr14:24759345..24761161-chr14:24766043..24768971,2	K562	blood:
7	chr14:24759955..24762103-chr14:24766475..24767984,2	K562	blood:
8	chr14:24766883..24768447-chr14:24900633..24902842,2	K562	blood:
9	chr14:24655120..24666858-chr14:24765577..24776253,24	MCF-7	breast:
10	chr14:24745018..24746771-chr14:24765412..24768322,2	K562	blood:
11	chr14:24766197..24768383-chr14:24901175..24902842,2	K562	blood:
12	chr14:24766841..24768982-chr14:24770722..24773085,2	MCF-7	breast:
13	chr14:24766883..24768123-chrX:15692539..15693561,3	Hela-S3	cervix:
14	chr14:24764989..24768278-chr14:24895035..24897150,3	K562	blood:
15	chr14:24767332..24771774-chr14:24910139..24913002,7	MCF-7	breast:
16	chr14:24767097..24775014-chr14:24779936..24787049,14	MCF-7	breast:
17	chr14:24709953..24714493-chr14:24766859..24769769,8	K562	blood:
18	chr14:24765284..24770509-chr14:24899183..24903551,4	MCF-7	breast:
19	chr14:24701050..24705855-chr14:24766597..24769956,4	K562	blood:
20	chr14:24617565..24619359-chr14:24765168..24767839,2	K562	blood:
21	chr14:24740761..24742611-chr14:24767431..24768980,2	K562	blood:
22	chr14:24767708..24770495-chr14:24910481..24913051,4	MCF-7	breast:
23	chr14:24759089..24762221-chr14:24766736..24770177,4	MCF-7	breast:
24	chr14:24738683..24743110-chr14:24766285..24769354,4	K562	blood:
25	chr14:24709953..24713670-chr14:24767111..24769746,6	K562	blood:
26	chr14:24629249..24631887-chr14:24767463..24769864,3	MCF-7	breast:
27	chr14:24766804..24771569-chr14:24898237..24903800,5	MCF-7	breast:
28	chr14:24765570..24768951-chr14:24773362..24777339,4	K562	blood:
29	chr14:24766317..24768502-chr19:39108568..39111298,2	MCF-7	breast:

No data

Variant related genes	Relation type
NOP9	TF binding region
DHRS1	TF binding region
ENSG00000136305	Chromatin interaction
ENSG00000254692	Chromatin interaction
ENSG00000186312	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000255526	Chromatin interaction
ENSG00000259522	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000104814	Chromatin interaction
ENSG00000129559	Chromatin interaction
ENSG00000213920	Chromatin interaction
ENSG00000100911	Chromatin interaction
ENSG00000100926	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000100938	Chromatin interaction
ENSG00000213928	Chromatin interaction
ENSG00000254505	Chromatin interaction
ENSG00000100445	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000092098	Chromatin interaction
ENSG00000178982	Chromatin interaction
ENSG00000196497	Chromatin interaction
ENSG00000139899	Chromatin interaction
ENSG00000260669	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000213903	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs1046587	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1051883	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12881984	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12884896	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12885593	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12887789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12891757	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12892146	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12892419	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12892579	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12895335	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12895752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12896386	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12896469	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295306	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295307	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982889	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4982890	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4982891	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4982892	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4982894	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7146665	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7400863	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7401804	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs747060	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8003991	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs941507	0.96[CEU][hapmap];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv901499	chr14:24765622-24787588	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a
4	nsv901500	chr14:24765622-24793762	Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	n/a

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs3825586	DHRS1	cis	Thyroid	GTEx
rs3825586	CMTM5	cis	cerebellum	SCAN
rs3825586	DHRS1	cis	parietal	SCAN
rs3825586	RABGGTA	cis	multi-tissue	Pritchard
rs3825586	MYH6	cis	cerebellum	SCAN
rs3825586	RNF31	cis	cerebellum	SCAN
rs3825586	TSSK4	cis	parietal	SCAN
rs3825586	DHRS1	cis	Frontal Cortex	GTEx
rs3825586	ANG	cis	parietal	SCAN
rs3825586	DHRS1	cis	cerebellum	SCAN
rs3825586	C14orf167	cis	intralobular white matter	BrainEAC
rs3825586	DHRS1	cis	multi-tissue	Pritchard
rs3825586	FAM158A	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24741200-24768200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:24741600-24767800	Weak transcription	Fetal Brain Male	brain
3	chr14:24748600-24768200	Weak transcription	Psoas Muscle	Psoas
4	chr14:24749000-24768200	Weak transcription	Right Atrium	heart
5	chr14:24753600-24768200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr14:24759800-24768000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr14:24761600-24767800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr14:24761800-24768400	Weak transcription	Small Intestine	intestine
9	chr14:24762000-24768000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr14:24762000-24768000	Weak transcription	Right Ventricle	heart
11	chr14:24765000-24768000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr14:24765400-24768000	Weak transcription	Brain Germinal Matrix	brain
13	chr14:24765400-24768200	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr14:24765600-24768000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr14:24765600-24768000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr14:24765600-24768000	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr14:24765600-24768000	Weak transcription	Fetal Brain Female	brain
18	chr14:24765800-24767800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr14:24765800-24767800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr14:24765800-24767800	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr14:24765800-24767800	Enhancers	Hela-S3	cervix
22	chr14:24765800-24767800	Enhancers	HMEC	breast
23	chr14:24765800-24768000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr14:24765800-24768000	Weak transcription	HUES48 Cell Line	embryonic stem cell
25	chr14:24765800-24768000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr14:24765800-24768000	Enhancers	Primary T helper cells fromperipheralblood	blood
27	chr14:24765800-24768000	Genic enhancers	Fetal Intestine Small	intestine
28	chr14:24765800-24768000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr14:24765800-24768000	Enhancers	Dnd41	blood
30	chr14:24765800-24768200	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr14:24765800-24768200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr14:24765800-24768200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:24765800-24768200	Weak transcription	Aorta	Aorta
34	chr14:24766000-24767800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr14:24766000-24767800	Weak transcription	Colonic Mucosa	Colon
36	chr14:24766000-24767800	Weak transcription	Rectal Smooth Muscle	rectum
37	chr14:24766000-24768000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr14:24766000-24768000	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr14:24766000-24768000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr14:24766000-24768000	Weak transcription	Colon Smooth Muscle	Colon
41	chr14:24766000-24768000	Weak transcription	Fetal Lung	lung
42	chr14:24766000-24768000	Weak transcription	Placenta	Placenta
43	chr14:24766000-24768000	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr14:24766000-24768200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr14:24766000-24768200	Enhancers	Primary B cells from peripheral blood	blood
46	chr14:24766000-24768200	Enhancers	Primary T helper naive cells from peripheral blood	blood
47	chr14:24766000-24768200	Enhancers	Fetal Thymus	thymus
48	chr14:24766200-24767800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr14:24766200-24767800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr14:24766200-24767800	Weak transcription	Fetal Stomach	stomach

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