Variant report

Variant	rs12537
Chromosome Location	chr22:30423460-30423461
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr22:30422072..30424953-chr22:30431511..30433741,2	MCF-7	breast:
2	chr22:30421468..30423711-chr22:30425219..30428106,3	K562	blood:
3	chr22:30421588..30423711-chr22:30425219..30427810,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1468177	0.84[EUR][1000 genomes]
rs2412960	0.80[CEU][hapmap]
rs2412963	0.80[CEU][hapmap]
rs2412974	0.88[EUR][1000 genomes]
rs36600	0.80[CEU][hapmap]
rs36604	0.80[CEU][hapmap]
rs3788423	0.80[CEU][hapmap]
rs3887275	0.80[CEU][hapmap]
rs41172	0.88[CEU][hapmap];0.85[TSI][hapmap];0.89[EUR][1000 genomes]
rs41174	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs41177	0.96[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41178	0.86[EUR][1000 genomes]
rs4239932	0.80[CEU][hapmap]
rs4823063	0.80[CEU][hapmap]
rs5753014	0.82[CHD][hapmap]
rs5763746	0.82[CHD][hapmap]
rs5763793	0.85[EUR][1000 genomes]
rs737909	0.80[CEU][hapmap]
rs737912	0.80[CEU][hapmap]
rs757026	0.82[CHD][hapmap]
rs9625921	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.89[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	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

Variant related diseases (count:1)

Disease	PMID	Source
IgA nephropathy	22197929	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12537	MTMR3	cis	multi-tissue	Pritchard
rs12537	MTMR3	cis	parietal	SCAN
rs12537	ASCC2	cis	cerebellum	SCAN
rs12537	NEFH	cis	cerebellum	SCAN
rs12537	CRYBB3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:30363400-30427800	Strong transcription	Monocytes-CD14+_RO01746	blood
2	chr22:30367000-30426600	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr22:30390200-30434200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr22:30391400-30433000	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr22:30392600-30425000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr22:30393800-30424800	Strong transcription	Primary T cells fromperipheralblood	blood
7	chr22:30394600-30424600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
8	chr22:30394800-30425200	Strong transcription	Fetal Intestine Large	intestine
9	chr22:30394800-30426200	Strong transcription	Placenta	Placenta
10	chr22:30396800-30426200	Strong transcription	Primary B cells from cord blood	blood
11	chr22:30397800-30423800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr22:30397800-30425400	Strong transcription	Primary B cells from peripheral blood	blood
13	chr22:30398000-30424400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr22:30398000-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr22:30398400-30425000	Strong transcription	Primary hematopoietic stem cells	blood
16	chr22:30398600-30425200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
17	chr22:30401600-30425200	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr22:30402200-30425200	Strong transcription	Primary T helper cells PMA-I stimulated	--
19	chr22:30402400-30424600	Strong transcription	Primary T helper cells fromperipheralblood	blood
20	chr22:30402600-30423600	Strong transcription	Liver	Liver
21	chr22:30402600-30426200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr22:30402800-30424200	Strong transcription	HUES6 Cell Line	embryonic stem cell
23	chr22:30402800-30425800	Strong transcription	Fetal Muscle Leg	muscle
24	chr22:30403000-30424400	Strong transcription	Fetal Brain Female	brain
25	chr22:30403000-30425200	Strong transcription	Stomach Smooth Muscle	stomach
26	chr22:30404400-30426400	Strong transcription	Primary T cells from cord blood	blood
27	chr22:30404800-30426000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr22:30405000-30424200	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr22:30405200-30424600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr22:30405200-30424800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr22:30405800-30424800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr22:30406000-30426600	Strong transcription	Thymus	Thymus
33	chr22:30406200-30425200	Strong transcription	Fetal Thymus	thymus
34	chr22:30407800-30425200	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr22:30408000-30425800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr22:30408200-30425000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr22:30408400-30423600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
38	chr22:30408400-30424200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
39	chr22:30408400-30425800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr22:30408600-30424600	Strong transcription	Rectal Smooth Muscle	rectum
41	chr22:30408800-30423800	Strong transcription	Ovary	ovary
42	chr22:30409000-30424200	Strong transcription	Pancreas	Pancrea
43	chr22:30409000-30432800	Strong transcription	Fetal Stomach	stomach
44	chr22:30410600-30424400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr22:30410600-30424800	Strong transcription	Colonic Mucosa	Colon
46	chr22:30410800-30424400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr22:30412000-30431200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr22:30413600-30425600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr22:30414200-30425200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr22:30415000-30425200	Strong transcription	NHLF	lung

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