Variant report

Variant	rs2412980
Chromosome Location	chr22:30592069-30592070
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:30590030..30593992-chr22:30596510..30599068,3	K562	blood:
2	chr22:30589990..30596479-chr22:30639909..30648381,15	MCF-7	breast:
3	chr22:30580247..30582662-chr22:30589957..30592306,3	K562	blood:
4	chr22:30578652..30582637-chr22:30590732..30593754,4	K562	blood:
5	chr11:9594464..9595108-chr22:30591798..30592673,2	Hela-S3	cervix:
6	chr22:30538829..30541820-chr22:30591024..30593094,2	K562	blood:
7	chr22:30584790..30588358-chr22:30588911..30595947,7	MCF-7	breast:
8	chr22:30587225..30588741-chr22:30589978..30592265,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000268812	Chromatin interaction
ENSG00000128342	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11552852	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13055101	0.82[EUR][1000 genomes]
rs16988244	1.00[CEU][hapmap];0.85[TSI][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988291	1.00[CEU][hapmap];0.85[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988303	1.00[CEU][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988304	1.00[CEU][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16988333	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17648208	0.91[EUR][1000 genomes]
rs1807726	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2412981	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs41278853	0.89[EUR][1000 genomes]
rs41281623	0.86[EUR][1000 genomes]
rs41281633	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4482600	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4482601	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs45629133	0.82[EUR][1000 genomes]
rs4823078	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56392746	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56406718	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5753038	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs5753039	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5753042	1.00[CEU][hapmap];0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5753043	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs5763855	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763856	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763857	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763858	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763870	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763873	1.00[CEU][hapmap];0.89[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs5763878	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58162368	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs5997597	0.83[TSI][hapmap]
rs6006383	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60759987	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6518681	1.00[EUR][1000 genomes]
rs6519802	0.92[LWK][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.87[EUR][1000 genomes]
rs6519805	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs713916	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7285585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7286205	1.00[CEU][hapmap];0.92[LWK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7290175	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs737901	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883354	0.80[EUR][1000 genomes]
rs73883355	0.80[EUR][1000 genomes]
rs73883359	0.84[EUR][1000 genomes]
rs73883360	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883363	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883367	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883370	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883374	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs73883375	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883377	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs73883378	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs8141471	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs962322	0.94[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[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	nsv1064081	chr22:29826745-30623965	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544677	chr22:29826745-30623965	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv834173	chr22:30515092-30658277	Enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv432239	chr22:30580161-30669883	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Dialysis-related mortality	21546767	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2412980	MTMR3	cis	multi-tissue	Pritchard

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30583800-30592200	Weak transcription	Small Intestine	intestine
2	chr22:30588200-30593600	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr22:30588600-30592200	Weak transcription	Thymus	Thymus
4	chr22:30589400-30592400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr22:30590400-30593400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
6	chr22:30590600-30592400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr22:30590800-30592600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr22:30590800-30593400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr22:30590800-30593600	Enhancers	Fetal Thymus	thymus
10	chr22:30591200-30593400	Enhancers	Stomach Mucosa	stomach
11	chr22:30591200-30593600	Enhancers	Fetal Stomach	stomach
12	chr22:30591200-30593800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr22:30591200-30593800	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr22:30591200-30595200	Enhancers	Breast Myoepithelial Primary Cells	Breast
15	chr22:30591400-30592200	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr22:30591400-30592200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr22:30591400-30592200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
18	chr22:30591400-30592200	Flanking Active TSS	Hela-S3	cervix
19	chr22:30591400-30592400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr22:30591400-30592400	Enhancers	HUES6 Cell Line	embryonic stem cell
21	chr22:30591400-30592600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr22:30591400-30592600	Enhancers	Brain Anterior Caudate	brain
23	chr22:30591400-30592600	Enhancers	Esophagus	oesophagus
24	chr22:30591400-30592600	Enhancers	Pancreas	Pancrea
25	chr22:30591400-30592600	Flanking Active TSS	HepG2	liver
26	chr22:30591400-30592800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr22:30591400-30592800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr22:30591400-30592800	Enhancers	Colon Smooth Muscle	Colon
29	chr22:30591400-30592800	Enhancers	Gastric	stomach
30	chr22:30591400-30593200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr22:30591400-30593200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr22:30591400-30593200	Enhancers	Right Atrium	heart
33	chr22:30591400-30593200	Enhancers	Sigmoid Colon	Sigmoid Colon
34	chr22:30591400-30593200	Enhancers	Spleen	Spleen
35	chr22:30591400-30593400	Enhancers	Fetal Intestine Small	intestine
36	chr22:30591400-30593400	Enhancers	Placenta	Placenta
37	chr22:30591400-30593600	Enhancers	Fetal Intestine Large	intestine
38	chr22:30591400-30594000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr22:30591400-30595000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
40	chr22:30591600-30592200	Flanking Active TSS	Primary B cells from cord blood	blood
41	chr22:30591600-30592200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
42	chr22:30591600-30592600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
43	chr22:30591600-30592800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr22:30591600-30592800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr22:30591600-30592800	Enhancers	Skeletal Muscle Female	skeletal muscle
46	chr22:30591600-30593000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr22:30591600-30593200	Enhancers	Primary B cells from peripheral blood	blood
48	chr22:30591600-30593200	Flanking Active TSS	HUVEC	blood vessel
49	chr22:30591600-30593400	Enhancers	Primary T helper cells fromperipheralblood	blood
50	chr22:30591600-30593400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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