Variant report

Variant	rs4424892
Chromosome Location	chr15:100104385-100104386
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SPI1	chr15:100104339-100104873	HL-60	blood:	n/a	n/a
2	MXI1	chr15:100104094-100104547	HepG2	liver:	n/a	n/a
3	MAX	chr15:100104385-100104910	H1-hESC	embryonic stem cell:	n/a	n/a
4	CTCF	chr15:100104320-100104470	AG10803	skin:	n/a	n/a
5	CTCF	chr15:100104380-100104530	HAc	cerebellar:	n/a	n/a
6	POLR2A	chr15:100104332-100107446	GM12878	blood:	n/a	n/a
7	MXI1	chr15:100104333-100107903	IMR90	lung:	n/a	chr15:100107634-100107649 chr15:100107636-100107651
8	POLR2A	chr15:100103790-100106469	GM12891	blood:	n/a	n/a
9	MAX	chr15:100104338-100106454	NB4	blood:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636

No.	Distal block	Cell Line	Cell type
1	chr15:100104091..100109623-chr15:100241901..100248412,10	MCF-7	breast:
2	chr15:100036529..100040308-chr15:100103797..100106516,3	MCF-7	breast:
3	chr15:100096994..100100303-chr15:100101564..100104656,5	K562	blood:
4	chr15:100101934..100104741-chr15:100233030..100234817,2	MCF-7	breast:

Variant related genes	Relation type
MEF2A	TF binding region
ENSG00000068305	Chromatin interaction
ENSG00000269810	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1019974	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs11247119	0.80[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs11852739	0.97[ASN][1000 genomes]
rs12593522	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap]
rs12899961	0.94[ASN][1000 genomes]
rs12901291	0.87[CEU][hapmap];1.00[JPT][hapmap]
rs12902009	0.85[ASN][1000 genomes]
rs12912791	0.90[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.85[MEX][hapmap];0.82[YRI][hapmap]
rs12916000	0.93[CEU][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs1434232	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs167805	0.91[JPT][hapmap];0.86[MEX][hapmap]
rs170522	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs188977	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap]
rs191256	0.82[JPT][hapmap]
rs2033546	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs2117309	0.81[CHB][hapmap]
rs2570807	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570808	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs2570816	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs2570823	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2570825	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2581467	0.87[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2581468	0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2581470	0.80[CEU][hapmap];0.90[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs2902349	0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs325381	0.82[JPT][hapmap]
rs325392	0.87[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.89[TSI][hapmap]
rs325404	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs325409	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs325410	0.80[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs325413	0.87[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4405533	0.96[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4421955	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4965529	0.81[AMR][1000 genomes]
rs7162392	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7165899	0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs7496677	0.87[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs892465	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1036346	chr15:99752391-100365458	Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
6	nsv542520	chr15:99752391-100365458	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
7	nsv1051560	chr15:99837102-100124483	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv817201	chr15:99839238-100537341	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
9	nsv904558	chr15:100019382-100171684	ZNF genes & repeats Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4424892	LYSMD4	cis	multi-tissue	Pritchard
rs4424892	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100088600-100105000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:100099200-100105200	Weak transcription	Aorta	Aorta
3	chr15:100099400-100104800	Weak transcription	HSMMtube	muscle
4	chr15:100102000-100104600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:100102000-100105000	Enhancers	Fetal Thymus	thymus
6	chr15:100102200-100104600	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr15:100102200-100104600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr15:100102200-100105000	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:100102200-100105000	Enhancers	Dnd41	blood
10	chr15:100102400-100105000	Enhancers	Primary hematopoietic stem cells	blood
11	chr15:100102400-100105200	Enhancers	Placenta	Placenta
12	chr15:100102600-100104800	Enhancers	Brain Substantia Nigra	brain
13	chr15:100102600-100105000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
14	chr15:100102600-100105200	Enhancers	Primary T cells from cord blood	blood
15	chr15:100102800-100104800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr15:100102800-100105000	Enhancers	H1 Cell Line	embryonic stem cell
17	chr15:100102800-100105000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr15:100103000-100104600	Weak transcription	Thymus	Thymus
19	chr15:100103000-100105000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr15:100103200-100105000	Enhancers	Primary T helper cells PMA-I stimulated	--
21	chr15:100103400-100104600	Enhancers	iPS-18 Cell Line	embryonic stem cell
22	chr15:100103400-100104800	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
23	chr15:100103400-100104800	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:100103600-100104400	Enhancers	HUES64 Cell Line	embryonic stem cell
25	chr15:100103600-100104600	Enhancers	Brain Anterior Caudate	brain
26	chr15:100103600-100104600	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr15:100103600-100104600	Enhancers	Skeletal Muscle Male	skeletal muscle
28	chr15:100103600-100104600	Bivalent Enhancer	HepG2	liver
29	chr15:100103600-100104800	Enhancers	ES-I3 Cell Line	embryonic stem cell
30	chr15:100103600-100104800	Enhancers	Brain Hippocampus Middle	brain
31	chr15:100103600-100105000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:100103600-100105000	Enhancers	HUES48 Cell Line	embryonic stem cell
33	chr15:100103600-100105000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:100103600-100105000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:100103600-100105000	Enhancers	Brain Inferior Temporal Lobe	brain
36	chr15:100103600-100105200	Enhancers	Primary B cells from cord blood	blood
37	chr15:100103600-100105200	Enhancers	Fetal Muscle Trunk	muscle
38	chr15:100103600-100105200	Enhancers	Right Atrium	heart
39	chr15:100103600-100105600	Enhancers	Spleen	Spleen
40	chr15:100103800-100104400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:100103800-100104400	Enhancers	Colon Smooth Muscle	Colon
42	chr15:100103800-100104600	Enhancers	Breast Myoepithelial Primary Cells	Breast
43	chr15:100103800-100104600	Enhancers	Adipose Nuclei	Adipose
44	chr15:100103800-100104600	Weak transcription	Lung	lung
45	chr15:100103800-100104800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:100103800-100104800	Enhancers	Rectal Smooth Muscle	rectum
47	chr15:100103800-100104800	Weak transcription	Right Ventricle	heart
48	chr15:100103800-100104800	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr15:100103800-100105000	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr15:100103800-100105000	Enhancers	Primary B cells from peripheral blood	blood

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