Variant report

Variant	rs10431505
Chromosome Location	chr12:58178589-58178590
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:58178480..58181770-chr12:58328004..58330583,3	K562	blood:
2	chr12:58176490..58178791-chr12:58333525..58336024,3	K562	blood:
3	chr12:58177143..58179601-chr12:58187871..58190318,2	K562	blood:

Variant related genes	Relation type
ENSG00000166896	Chromatin interaction
ENSG00000257698	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 11 )

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

rs_ID	r²[population]
rs1021469	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10431552	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10747783	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10783847	0.95[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10783848	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877012	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10877013	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10877014	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877015	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877016	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877017	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877018	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10877019	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10877022	0.82[AFR][1000 genomes]
rs11172333	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172335	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172342	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172343	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11172344	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11172349	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11172350	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11172351	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1599932	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1875124	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2014886	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2069502	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2069506	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2072052	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291617	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3782130	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3825079	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4646536	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56177740	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs703842	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs724834	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7965287	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8181644	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs923829	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9652011	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[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:11)

SNP	Gene	Cis/trans	Tissue	Source
rs10431505	METTL21B	cis	Esophagus Muscularis	GTEx
rs10431505	METTL21B	cis	lung	GTEx
rs10431505	TSFM	cis	Muscle Skeletal	GTEx
rs10431505	XRCC6BP1	cis	Muscle Skeletal	GTEx
rs10431505	METTL21B	cis	Adipose Subcutaneous	GTEx
rs10431505	TSFM	cis	multi-tissue	Pritchard
rs10431505	METTL21B	cis	Whole Blood	GTEx
rs10431505	METTL21B	cis	Nerve Tibial	GTEx
rs10431505	METTL21B	cis	Skin Sun Exposed Lower leg	GTEx
rs10431505	TSFM	Cis_1M	lymphoblastoid	RTeQTL
rs10431505	FAM119B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:58177200-58179000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:58177200-58179000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:58177200-58179800	Weak transcription	Aorta	Aorta
4	chr12:58177200-58189800	Weak transcription	Small Intestine	intestine
5	chr12:58177200-58197200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:58177400-58179000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr12:58177400-58179000	Weak transcription	Left Ventricle	heart
8	chr12:58177400-58179000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:58177400-58179000	Weak transcription	NH-A	brain
10	chr12:58177400-58179200	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:58177400-58179200	Weak transcription	HSMMtube	muscle
12	chr12:58177400-58180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr12:58177400-58180000	Weak transcription	Colonic Mucosa	Colon
14	chr12:58177400-58180000	Weak transcription	Ovary	ovary
15	chr12:58177400-58180000	Weak transcription	Psoas Muscle	Psoas
16	chr12:58177400-58180000	Weak transcription	Spleen	Spleen
17	chr12:58177400-58180200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr12:58177400-58180200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr12:58177400-58190000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr12:58177400-58192800	Weak transcription	Stomach Mucosa	stomach
21	chr12:58177400-58200400	Weak transcription	Fetal Heart	heart
22	chr12:58177400-58216400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr12:58177600-58179000	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr12:58177600-58179000	Weak transcription	Brain Anterior Caudate	brain
25	chr12:58177600-58179000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr12:58177600-58179200	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr12:58177600-58179400	Weak transcription	Fetal Brain Male	brain
28	chr12:58177600-58179600	Weak transcription	Gastric	stomach
29	chr12:58177600-58179800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr12:58177600-58179800	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr12:58177600-58186400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:58177800-58178600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr12:58177800-58178600	Weak transcription	Lung	lung
34	chr12:58177800-58179000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr12:58177800-58179000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr12:58177800-58179000	Weak transcription	Thymus	Thymus
37	chr12:58177800-58179400	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr12:58177800-58179600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr12:58177800-58179600	Weak transcription	Pancreas	Pancrea
40	chr12:58177800-58179800	Weak transcription	Esophagus	oesophagus
41	chr12:58177800-58182600	Strong transcription	Placenta	Placenta
42	chr12:58177800-58184000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr12:58177800-58187400	Strong transcription	Osteobl	bone
44	chr12:58177800-58188400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:58177800-58189600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr12:58177800-58191200	Strong transcription	HUES48 Cell Line	embryonic stem cell
47	chr12:58177800-58192200	Strong transcription	HUES64 Cell Line	embryonic stem cell
48	chr12:58177800-58198400	Strong transcription	Fetal Muscle Trunk	muscle
49	chr12:58177800-58198400	Strong transcription	Fetal Muscle Leg	muscle
50	chr12:58177800-58199000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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