Variant report

Variant	rs892465
Chromosome Location	chr15:100105185-100105186
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	MAX	chr15:100104636-100107183	HepG2	liver:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636
2	POLR2A	chr15:100104866-100107196	GM18526	blood:	n/a	n/a
3	POLR2A	chr15:100104893-100106445	MCF10A-Er-Src	breast:	n/a	n/a
4	NR2F2	chr15:100105089-100105634	MCF-7	breast:	n/a	n/a
5	ZNF143	chr15:100104943-100106392	Hela-S3	cervix:	n/a	chr15:100105667-100105677
6	POLR2A	chr15:100105043-100107600	IMR90	lung:	n/a	n/a
7	MAZ	chr15:100105134-100107727	IMR90	lung:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636
8	EP300	chr15:100105161-100106560	ECC-1	luminal epithelium:	n/a	chr15:100106361-100106370 chr15:100106281-100106297 chr15:100105661-100105677
9	POLR2A	chr15:100104650-100106558	GM12878	blood:	n/a	n/a
10	MAZ	chr15:100105079-100106416	K562	blood:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636
11	POLR2A	chr15:100104544-100107315	Raji	blood:	n/a	n/a
12	CEBPB	chr15:100104935-100105553	MCF-7	breast:	n/a	n/a
13	POLR2A	chr15:100105184-100105388	GM12891	blood:	n/a	n/a
14	SIN3A	chr15:100104521-100106405	H1-hESC	embryonic stem cell:	n/a	chr15:100106317-100106330
15	STAT5A	chr15:100104508-100105497	GM12878	blood:	n/a	chr15:100104647-100104655
16	POLR2A	chr15:100105162-100105545	PANC-1	pancreas:	n/a	n/a
17	MAX	chr15:100105030-100106557	A549	lung:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636
18	EP300	chr15:100105107-100105306	HepG2	liver:	n/a	n/a
19	POLR2A	chr15:100104580-100106514	GM12878	blood:	n/a	n/a
20	NR2F2	chr15:100104909-100106432	MCF-7	breast:	n/a	n/a
21	SMC3	chr15:100104965-100106386	Hela-S3	cervix:	n/a	chr15:100106253-100106260
22	POLR2A	chr15:100104543-100107408	GM18505	blood:	n/a	n/a
23	JUND	chr15:100105037-100106342	K562	blood:	n/a	n/a
24	MYC	chr15:100105065-100106452	K562	blood:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636
25	CREB1	chr15:100105091-100106524	HepG2	liver:	n/a	n/a
26	POLR2A	chr15:100104827-100107518	Hela-S3	cervix:	n/a	n/a
27	POLR2A	chr15:100104950-100106425	Hela-S3	cervix:	n/a	n/a
28	ESR1	chr15:100105097-100105888	ECC-1	luminal epithelium:	n/a	n/a
29	ZNF263	chr15:100104509-100106309	HEK293-T-REx	kidney:	n/a	chr15:100104647-100104656 chr15:100105461-100105470
30	MAX	chr15:100104831-100106571	A549	lung:	n/a	chr15:100105913-100105922 chr15:100105610-100105619 chr15:100105627-100105636
31	RFX5	chr15:100105169-100106374	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr15:100105146-100106530	HUVEC	blood vessel:	n/a	n/a
33	TCF12	chr15:100105107-100106563	ECC-1	luminal epithelium:	n/a	chr15:100106290-100106300 chr15:100105388-100105395 chr15:100106289-100106296
34	TCF3	chr15:100105179-100105901	GM12878	blood:	n/a	n/a
35	MXI1	chr15:100104968-100108088	SK-N-SH	brain:	n/a	chr15:100107634-100107649 chr15:100107636-100107651
36	RELA	chr15:100104578-100106395	GM15510	blood:	n/a	n/a
37	POLR2A	chr15:100104530-100107155	GM18951	blood:	n/a	n/a
38	ELK1	chr15:100105128-100105350	Hela-S3	cervix:	n/a	n/a
39	POLR2A	chr15:100104771-100106516	GM12892	blood:	n/a	n/a
40	CHD1	chr15:100105106-100108685	IMR90	lung:	n/a	chr15:100105377-100105387
41	SMARCB1	chr15:100104696-100107228	Hela-S3	cervix:	n/a	n/a
42	EBF1	chr15:100105010-100105633	GM12878	blood:	n/a	n/a
43	CCNT2	chr15:100105061-100106462	K562	blood:	n/a	chr15:100106392-100106401
44	POLR2A	chr15:100104906-100107166	GM12878	blood:	n/a	n/a
45	POLR2A	chr15:100104493-100107234	GM12892	blood:	n/a	n/a
46	RELA	chr15:100104800-100106354	GM12891	blood:	n/a	n/a
47	POLR2A	chr15:100105148-100106506	ECC-1	luminal epithelium:	n/a	n/a
48	RELA	chr15:100105053-100106397	GM12892	blood:	n/a	n/a
49	RUNX3	chr15:100104534-100105495	GM12878	blood:	n/a	n/a
50	ATF2	chr15:100104867-100105379	GM12878	blood:	n/a	n/a

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	chr15:99826876..99828722-chr15:100104864..100106375,2	MCF-7	breast:
4	chr15:100104936..100107605-chr15:100221549..100224496,2	MCF-7	breast:
5	chr15:100104819..100107629-chr15:100257615..100260464,2	MCF-7	breast:

Variant related genes	Relation type
MEF2A	TF binding region
ENSG00000269810	Chromatin interaction
ENSG00000068305	Chromatin interaction
ENSG00000168904	Chromatin interaction
ENSG00000201724	Chromatin interaction
ENSG00000214397	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1019974	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11247119	1.00[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.84[YRI][hapmap]
rs11852739	0.95[ASN][1000 genomes]
rs12593522	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap]
rs12899961	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12901291	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs12902009	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12912791	0.95[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.81[EUR][1000 genomes]
rs12916000	0.80[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1434232	0.83[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs167805	0.92[ASW][hapmap];0.80[CHB][hapmap];0.81[CHD][hapmap];0.91[JPT][hapmap];0.86[MEX][hapmap]
rs170522	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs188977	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs191256	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2033546	1.00[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.91[MEX][hapmap];0.91[YRI][hapmap]
rs2117309	0.86[CHB][hapmap]
rs2570807	0.88[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2570808	0.91[ASW][hapmap];0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[YRI][hapmap]
rs2570816	0.93[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2570823	0.90[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2570825	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2581467	0.81[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2581468	0.93[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2581470	0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.80[TSI][hapmap]
rs2902349	0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs325381	0.82[JPT][hapmap]
rs325392	1.00[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs325404	0.90[CHB][hapmap];0.91[JPT][hapmap]
rs325409	1.00[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs325410	1.00[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs325411	0.83[ASW][hapmap]
rs325413	0.92[ASW][hapmap];0.85[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4405533	0.99[ASN][1000 genomes]
rs4421955	0.88[ASN][1000 genomes]
rs4424892	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.97[ASN][1000 genomes]
rs4965529	0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7162392	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7165899	0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7496677	0.92[ASW][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.86[MEX][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs892465	LYSMD4	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:100099200-100105200	Weak transcription	Aorta	Aorta
2	chr15:100102400-100105200	Enhancers	Placenta	Placenta
3	chr15:100102600-100105200	Enhancers	Primary T cells from cord blood	blood
4	chr15:100103600-100105200	Enhancers	Primary B cells from cord blood	blood
5	chr15:100103600-100105200	Enhancers	Fetal Muscle Trunk	muscle
6	chr15:100103600-100105200	Enhancers	Right Atrium	heart
7	chr15:100103600-100105600	Enhancers	Spleen	Spleen
8	chr15:100103800-100105200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:100103800-100105200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr15:100104000-100105200	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr15:100104000-100105200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:100104000-100105200	Enhancers	Fetal Muscle Leg	muscle
13	chr15:100104200-100105200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:100104200-100105200	Enhancers	Fetal Lung	lung
15	chr15:100104200-100105200	Enhancers	Fetal Stomach	stomach
16	chr15:100104200-100105200	Enhancers	Left Ventricle	heart
17	chr15:100104200-100105200	Enhancers	Psoas Muscle	Psoas
18	chr15:100104200-100105400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr15:100104200-100105600	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr15:100104400-100105200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:100104400-100105200	Enhancers	Fetal Intestine Small	intestine
22	chr15:100104400-100105200	Enhancers	Pancreas	Pancrea
23	chr15:100104400-100105200	Enhancers	HUVEC	blood vessel
24	chr15:100104400-100105200	Enhancers	NH-A	brain
25	chr15:100104400-100105400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr15:100104400-100105400	Flanking Active TSS	Colon Smooth Muscle	Colon
27	chr15:100104600-100105200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
28	chr15:100104600-100105200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:100104600-100105200	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr15:100104600-100105200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:100104600-100105200	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr15:100104600-100105200	Enhancers	Esophagus	oesophagus
33	chr15:100104600-100105200	Enhancers	Fetal Intestine Large	intestine
34	chr15:100104600-100105200	Enhancers	Lung	lung
35	chr15:100104600-100105200	Enhancers	Stomach Mucosa	stomach
36	chr15:100104600-100105200	Flanking Bivalent TSS/Enh	HepG2	liver
37	chr15:100104600-100105200	Enhancers	HMEC	breast
38	chr15:100104600-100105400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr15:100104600-100105400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
40	chr15:100104600-100105400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:100104600-100105400	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr15:100104600-100105400	Flanking Active TSS	Brain Anterior Caudate	brain
43	chr15:100104600-100105400	Flanking Active TSS	Brain Cingulate Gyrus	brain
44	chr15:100104600-100105400	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:100104600-100105400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
46	chr15:100104600-100105600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:100104600-100105600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:100104800-100105200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
49	chr15:100104800-100105200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr15:100104800-100105200	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

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