Variant report

Variant	rs56287938
Chromosome Location	chr17:45297913-45297914
allele	C/G
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	BHLHE40	chr17:45297886-45298263	GM12878	blood:	n/a	n/a
2	POLR2A	chr17:45297901-45298232	H1-neurons	neurons:	n/a	n/a
3	EP300	chr17:45297868-45298175	GM12878	blood:	n/a	chr17:45298099-45298112
4	POLR2A	chr17:45297910-45298303	H1-neurons	neurons:	n/a	n/a

Variant related genes	Relation type
ENSG00000252088	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11570481	0.85[AFR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11570495	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11570513	0.82[ASN][1000 genomes]
rs11570548	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16941626	0.86[ASN][1000 genomes]
rs16941628	0.86[ASN][1000 genomes]
rs16941635	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs16941671	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1986817	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55706273	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55887846	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59349147	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs717162	0.90[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	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs56287938	MYL4	cis	Esophagus Muscularis	GTEx
rs56287938	MYL4	cis	lung	GTEx

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45288400-45302000	Weak transcription	HSMM	muscle
2	chr17:45293400-45299000	Enhancers	Primary T killer memory cells from peripheral blood	blood
3	chr17:45293600-45298600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
4	chr17:45293600-45298600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr17:45293600-45298600	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr17:45293600-45298800	Enhancers	Primary T helper cells PMA-I stimulated	--
7	chr17:45293600-45299000	Enhancers	Primary T cells fromperipheralblood	blood
8	chr17:45294000-45298800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr17:45294000-45299000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr17:45294000-45299000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr17:45294000-45299000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr17:45294200-45298000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:45294200-45298600	Enhancers	Primary T cells from cord blood	blood
14	chr17:45294200-45299600	Enhancers	Primary B cells from peripheral blood	blood
15	chr17:45295000-45298000	Weak transcription	HSMMtube	muscle
16	chr17:45295400-45299200	Enhancers	Primary hematopoietic stem cells	blood
17	chr17:45295600-45301800	Enhancers	Fetal Intestine Small	intestine
18	chr17:45295800-45298400	Enhancers	Right Ventricle	heart
19	chr17:45295800-45298800	Genic enhancers	Fetal Muscle Leg	muscle
20	chr17:45295800-45299000	Enhancers	Fetal Thymus	thymus
21	chr17:45295800-45299200	Enhancers	Primary B cells from cord blood	blood
22	chr17:45296200-45298200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr17:45296200-45298200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
24	chr17:45296200-45298200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr17:45296200-45298400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr17:45296200-45298800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr17:45296200-45299200	Genic enhancers	Fetal Muscle Trunk	muscle
28	chr17:45296200-45299200	Enhancers	Dnd41	blood
29	chr17:45296400-45299000	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr17:45296400-45304000	Enhancers	Stomach Mucosa	stomach
31	chr17:45296400-45305000	Enhancers	Spleen	Spleen
32	chr17:45296600-45298200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr17:45296600-45298400	Enhancers	GM12878-XiMat	blood
34	chr17:45296800-45298200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr17:45296800-45299200	Weak transcription	Small Intestine	intestine
36	chr17:45296800-45300200	Weak transcription	Adipose Nuclei	Adipose
37	chr17:45297200-45298000	Transcr. at gene 5' and 3'	K562	blood
38	chr17:45297200-45299200	Weak transcription	Fetal Intestine Large	intestine
39	chr17:45297200-45300200	Weak transcription	Right Atrium	heart
40	chr17:45297400-45298400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr17:45297400-45298400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
42	chr17:45297400-45298400	Enhancers	Fetal Brain Female	brain
43	chr17:45297400-45298600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr17:45297400-45298600	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr17:45297400-45299000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr17:45297600-45298200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr17:45297600-45298200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
48	chr17:45297600-45298200	Genic enhancers	Fetal Heart	heart
49	chr17:45297600-45298400	Enhancers	H9 Cell Line	embryonic stem cell
50	chr17:45297600-45298400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell

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