Variant report

Variant	rs1599932
Chromosome Location	chr12:58177943-58177944
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58176542..58178155-chr12:58239377..58241593,2	K562	blood:
2	chr12:58176803..58178403-chr12:58230455..58233005,2	K562	blood:
3	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
4	chr12:58177143..58179601-chr12:58187871..58190318,2	K562	blood:
5	chr12:58146595..58149356-chr12:58175469..58178051,2	K562	blood:
6	chr12:58176873..58178429-chr12:58205054..58207229,2	MCF-7	breast:
7	chr12:58175049..58178042-chr12:58240093..58242141,3	K562	blood:

Variant related genes	Relation type
ENSG00000175215	Chromatin interaction
ENSG00000166896	Chromatin interaction
ENSG00000257953	Chromatin interaction
ENSG00000139266	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1021469	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10431505	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10431552	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10747783	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10783847	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10783848	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877011	0.83[EUR][1000 genomes]
rs10877012	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10877013	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877014	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877015	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877016	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10877017	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10877018	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10877019	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172333	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11172335	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172342	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172343	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11172344	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11172349	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11172350	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172351	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1875124	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2014886	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2069502	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2069506	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2072052	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2291617	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3782130	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3825079	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4646536	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56177740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs703842	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs724834	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965287	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8181644	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs923829	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9652011	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]

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	nsv510601	chr12:58130298-58191925	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv470297	chr12:58133256-58202419	Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv559046	chr12:58162085-58478598	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	261 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1599932	FAM119B	Cis_1M	lymphoblastoid	RTeQTL
rs1599932	TSFM	cis	Muscle Skeletal	GTEx
rs1599932	METTL21B	cis	Esophagus Muscularis	GTEx
rs1599932	CYP27B1	cis	Thyroid	GTEx
rs1599932	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs1599932	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs1599932	RP11-571M6.13	cis	Thyroid	GTEx
rs1599932	METTL21B	cis	Adipose Subcutaneous	GTEx
rs1599932	METTL21B	cis	Muscle Skeletal	GTEx
rs1599932	METTL21B	cis	lung	GTEx
rs1599932	METTL21B	cis	Whole Blood	GTEx
rs1599932	METTL21B	cis	Heart Left Ventricle	GTEx
rs1599932	TSFM	cis	multi-tissue	Pritchard
rs1599932	METTL21B	cis	Esophagus Mucosa	GTEx
rs1599932	TSFM	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58176400-58178000	Active TSS	NHLF	lung
2	chr12:58176600-58178200	Transcr. at gene 5' and 3'	Dnd41	blood
3	chr12:58177000-58178000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
4	chr12:58177000-58178000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr12:58177200-58178200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr12:58177200-58179000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:58177200-58179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr12:58177200-58179800	Weak transcription	Aorta	Aorta
9	chr12:58177200-58189800	Weak transcription	Small Intestine	intestine
10	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr12:58177400-58178000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr12:58177400-58178000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
13	chr12:58177400-58178000	Genic enhancers	Primary B cells from peripheral blood	blood
14	chr12:58177400-58178000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
15	chr12:58177400-58178000	Enhancers	Primary T killer memory cells from peripheral blood	blood
16	chr12:58177400-58178000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:58177400-58178000	Enhancers	Brain Cingulate Gyrus	brain
18	chr12:58177400-58178000	Enhancers	Brain Hippocampus Middle	brain
19	chr12:58177400-58178000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr12:58177400-58178000	Enhancers	Colon Smooth Muscle	Colon
21	chr12:58177400-58178000	Enhancers	Fetal Kidney	kidney
22	chr12:58177400-58178000	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr12:58177400-58178000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
24	chr12:58177400-58178200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:58177400-58178200	Enhancers	Primary B cells from cord blood	blood
26	chr12:58177400-58178200	Enhancers	Primary T cells from cord blood	blood
27	chr12:58177400-58178200	Enhancers	Primary hematopoietic stem cells	blood
28	chr12:58177400-58178200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr12:58177400-58178200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr12:58177400-58178200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr12:58177400-58178200	Enhancers	Adipose Nuclei	Adipose
32	chr12:58177400-58178200	Enhancers	Brain Angular Gyrus	brain
33	chr12:58177400-58178200	Enhancers	HUVEC	blood vessel
34	chr12:58177400-58178400	Weak transcription	Fetal Stomach	stomach
35	chr12:58177400-58179000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr12:58177400-58179000	Weak transcription	Left Ventricle	heart
37	chr12:58177400-58179000	Weak transcription	Monocytes-CD14+_RO01746	blood
38	chr12:58177400-58179000	Weak transcription	NH-A	brain
39	chr12:58177400-58179200	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:58177400-58179200	Weak transcription	HSMMtube	muscle
41	chr12:58177400-58180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr12:58177400-58180000	Weak transcription	Colonic Mucosa	Colon
43	chr12:58177400-58180000	Weak transcription	Ovary	ovary
44	chr12:58177400-58180000	Weak transcription	Psoas Muscle	Psoas
45	chr12:58177400-58180000	Weak transcription	Spleen	Spleen
46	chr12:58177400-58180200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
47	chr12:58177400-58180200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr12:58177400-58190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
49	chr12:58177400-58192800	Weak transcription	Stomach Mucosa	stomach
50	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart

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