Variant report

Variant	rs12892579
Chromosome Location	chr14:24759102-24759103
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:24740622..24743087-chr14:24757259..24759427,3	K562	blood:
2	chr14:24759089..24762221-chr14:24766736..24770177,4	MCF-7	breast:
3	chr14:24701726..24703938-chr14:24757883..24760008,2	K562	blood:
4	chr14:24752462..24755540-chr14:24756043..24759488,4	K562	blood:

Variant related genes	Relation type
ENSG00000100938	Chromatin interaction
ENSG00000196943	Chromatin interaction
ENSG00000157379	Chromatin interaction
ENSG00000100949	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 13 )

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

rs_ID	r²[population]
rs1046587	1.00[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.87[EUR][1000 genomes]
rs1051883	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12881984	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12884896	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12885593	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887789	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12891757	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12892146	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12892419	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12895335	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12895752	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12896386	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12896469	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295306	0.84[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295307	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3825586	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]
rs4982889	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982890	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4982891	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4982892	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4982894	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7146665	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7400863	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7401804	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs747060	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8003991	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs941507	0.96[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs12892579	RNF31	cis	cerebellum	SCAN
rs12892579	RABGGTA	cis	multi-tissue	Pritchard
rs12892579	TSSK4	cis	parietal	SCAN
rs12892579	DHRS1	cis	Frontal Cortex	GTEx
rs12892579	CMTM5	cis	cerebellum	SCAN
rs12892579	DHRS1	cis	Thyroid	GTEx
rs12892579	FAM158A	cis	parietal	SCAN
rs12892579	DHRS1	cis	parietal	SCAN
rs12892579	MYH6	cis	cerebellum	SCAN
rs12892579	DHRS1	cis	brain	seeQTL
rs12892579	DHRS1	cis	multi-tissue	Pritchard
rs12892579	ANG	cis	parietal	SCAN
rs12892579	DHRS1	cis	cerebellum	SCAN

Chromatin state (count:123 , 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	chr14:24741600-24759200	Weak transcription	Small Intestine	intestine
3	chr14:24741600-24767800	Weak transcription	Fetal Brain Male	brain
4	chr14:24748000-24764800	Weak transcription	K562	blood
5	chr14:24748600-24768200	Weak transcription	Psoas Muscle	Psoas
6	chr14:24748800-24764800	Weak transcription	Muscle Satellite Cultured Cells	--
7	chr14:24749000-24768200	Weak transcription	Right Atrium	heart
8	chr14:24749200-24759400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr14:24749400-24759400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr14:24749400-24763800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr14:24750600-24759200	Weak transcription	Left Ventricle	heart
12	chr14:24750800-24765000	Weak transcription	NHDF-Ad	bronchial
13	chr14:24752400-24759200	Weak transcription	Fetal Lung	lung
14	chr14:24753200-24760400	Weak transcription	Hela-S3	cervix
15	chr14:24753600-24766000	Weak transcription	Fetal Heart	heart
16	chr14:24753600-24768200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr14:24754200-24761400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr14:24756200-24765800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr14:24756400-24760600	Strong transcription	HepG2	liver
20	chr14:24756400-24764400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr14:24756400-24765800	Strong transcription	Fetal Intestine Small	intestine
22	chr14:24757200-24759200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr14:24757200-24764800	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr14:24757400-24759200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr14:24757400-24765000	Weak transcription	Fetal Kidney	kidney
26	chr14:24757600-24766000	Weak transcription	Stomach Mucosa	stomach
27	chr14:24757800-24766200	Strong transcription	Fetal Stomach	stomach
28	chr14:24758000-24762200	Strong transcription	NHEK	skin
29	chr14:24758000-24765400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr14:24758000-24766000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr14:24758400-24759800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
32	chr14:24758400-24759800	Genic enhancers	GM12878-XiMat	blood
33	chr14:24758400-24761200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr14:24758400-24762000	Strong transcription	Osteobl	bone
35	chr14:24758400-24762200	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr14:24758400-24762200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr14:24758400-24762400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:24758400-24762400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr14:24758400-24765200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr14:24758400-24766000	Strong transcription	Fetal Intestine Large	intestine
41	chr14:24758400-24766400	Strong transcription	Fetal Muscle Trunk	muscle
42	chr14:24758600-24759400	Strong transcription	Primary hematopoietic stem cells	blood
43	chr14:24758600-24759400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr14:24758600-24759800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr14:24758600-24759800	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr14:24758600-24759800	Genic enhancers	Primary B cells from cord blood	blood
47	chr14:24758600-24759800	Genic enhancers	Primary T cells fromperipheralblood	blood
48	chr14:24758600-24759800	Strong transcription	Liver	Liver
49	chr14:24758600-24760200	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr14:24758600-24760200	Strong transcription	NH-A	brain

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