Variant report

Variant	rs6493515
Chromosome Location	chr15:52010807-52010808
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	CEBPB	chr15:52010726-52010917	Hela-S3	cervix:	n/a	chr15:52010800-52010811
2	CEBPB	chr15:52010724-52010926	A549	lung:	n/a	chr15:52010800-52010811
3	CEBPB	chr15:52010618-52011003	K562	blood:	n/a	chr15:52010800-52010811
4	CEBPB	chr15:52010707-52010939	K562	blood:	n/a	chr15:52010800-52010811
5	CEBPB	chr15:52010675-52010910	IMR90	lung:	n/a	chr15:52010800-52010811
6	CEBPB	chr15:52010640-52010939	HepG2	liver:	n/a	chr15:52010800-52010811

No.	Distal block	Cell Line	Cell type
1	chr15:52010154..52013648-chr15:52016687..52020314,4	MCF-7	breast:
2	chr15:52008451..52011571-chr15:52027342..52031770,5	MCF-7	breast:
3	chr15:51970627..51972181-chr15:52008855..52011853,2	MCF-7	breast:
4	chr15:52005121..52007607-chr15:52009049..52011407,2	K562	blood:

Variant related genes	Relation type
ENSG00000259296	TF binding region
ENSG00000259296	Chromatin interaction
ENSG00000140280	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1001690	0.85[AMR][1000 genomes]
rs11070864	0.95[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1133882	1.00[YRI][hapmap]
rs11630084	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11632106	0.80[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11636345	0.81[EUR][1000 genomes]
rs11638766	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11638820	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs12917133	0.81[EUR][1000 genomes]
rs1350174	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1466276	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs1545602	0.80[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs1902430	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2034857	0.81[EUR][1000 genomes]
rs2034858	0.81[EUR][1000 genomes]
rs2077743	1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2168475	0.93[ASN][1000 genomes]
rs2414116	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2414117	0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4238383	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4502160	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs4622456	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4774602	0.81[EUR][1000 genomes]
rs4775978	0.81[EUR][1000 genomes]
rs526556	0.92[ASN][1000 genomes]
rs6493518	0.83[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs6493519	0.81[EUR][1000 genomes]
rs689884	0.85[EUR][1000 genomes]
rs7163176	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7165585	1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7166110	0.84[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs7173375	0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs7181553	0.84[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs8024081	0.81[EUR][1000 genomes]
rs8024088	0.81[EUR][1000 genomes]
rs8024589	0.81[EUR][1000 genomes]
rs8028258	1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv471243	chr15:51345485-52018096	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6493515	LYSMD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51974200-52018800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:51974600-52016400	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr15:51975600-52017200	Weak transcription	Fetal Brain Male	brain
4	chr15:51983000-52013200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:51984800-52018600	Weak transcription	Brain Hippocampus Middle	brain
6	chr15:51990000-52016800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
7	chr15:51991400-52018800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:51992200-52018800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr15:51993600-52016800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:51995400-52013200	Weak transcription	Brain Substantia Nigra	brain
11	chr15:51999800-52018200	Weak transcription	Fetal Stomach	stomach
12	chr15:52000000-52013800	Weak transcription	Colon Smooth Muscle	Colon
13	chr15:52000800-52024000	Weak transcription	Gastric	stomach
14	chr15:52001000-52018600	Weak transcription	Pancreas	Pancrea
15	chr15:52001200-52013000	Weak transcription	Fetal Muscle Trunk	muscle
16	chr15:52001600-52012000	Weak transcription	Primary B cells from cord blood	blood
17	chr15:52002400-52013600	Strong transcription	Fetal Brain Female	brain
18	chr15:52002800-52016600	Weak transcription	Pancreatic Islets	Pancreatic Islet
19	chr15:52003400-52013200	Weak transcription	Aorta	Aorta
20	chr15:52004000-52013400	Strong transcription	Brain Germinal Matrix	brain
21	chr15:52004400-52016400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr15:52004800-52012600	Weak transcription	Primary T cells from cord blood	blood
23	chr15:52004800-52018600	Weak transcription	Spleen	Spleen
24	chr15:52006200-52013000	Weak transcription	Esophagus	oesophagus
25	chr15:52006400-52013800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:52006400-52018400	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:52006600-52012000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr15:52006800-52013400	Weak transcription	K562	blood
29	chr15:52007000-52023400	Weak transcription	Brain Anterior Caudate	brain
30	chr15:52007400-52013000	Weak transcription	Dnd41	blood
31	chr15:52007400-52013400	Enhancers	Fetal Intestine Large	intestine
32	chr15:52007600-52013400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:52007600-52016800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:52007800-52016800	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:52007800-52018200	Weak transcription	NHDF-Ad	bronchial
36	chr15:52008000-52013400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:52008200-52023200	Weak transcription	Rectal Mucosa Donor 29	rectum
38	chr15:52008400-52018400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:52008400-52023400	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr15:52008800-52012800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:52008800-52016600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr15:52009000-52012400	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr15:52009000-52013400	Weak transcription	Brain Angular Gyrus	brain
44	chr15:52009000-52016600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:52009600-52011400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
46	chr15:52009600-52011800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:52009600-52014000	Enhancers	Fetal Intestine Small	intestine
48	chr15:52009800-52011400	Strong transcription	Brain Cingulate Gyrus	brain
49	chr15:52010000-52013000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:52010000-52013400	Enhancers	Duodenum Mucosa	Duodenum

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