Variant report

Variant	rs643875
Chromosome Location	chr15:41147093-41147094
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41147027..41152625-chr15:41184304..41188925,8	K562	blood:

Variant related genes	Relation type
ENSG00000104142	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1049598	0.93[CEU][hapmap]
rs17649	0.93[CEU][hapmap]
rs3736287	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4924508	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs582639	0.86[EUR][1000 genomes]
rs659232	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs661745	0.86[EUR][1000 genomes]
rs689626	0.93[CEU][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690458	0.93[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs690467	0.86[EUR][1000 genomes]
rs8028552	1.00[CEU][hapmap];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	esv1819092	chr15:41017682-41255750	Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
3	nsv904102	chr15:41046883-41201699	Strong transcription Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv1054764	chr15:41068625-41196410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv569228	chr15:41106485-41194151	Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
6	nsv904103	chr15:41123172-41275014	Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs643875	RP11-111A22.1	cis	Artery Tibial	GTEx
rs643875	PLCB2	cis	uninvolved skin	skin_eQTL
rs643875	C15orf57	cis	Artery Tibial	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:41137400-41152200	Weak transcription	Small Intestine	intestine
2	chr15:41137400-41165800	Weak transcription	Right Atrium	heart
3	chr15:41140000-41149800	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr15:41140000-41149800	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr15:41140000-41150400	Strong transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:41140200-41148000	Weak transcription	Spleen	Spleen
7	chr15:41140200-41149600	Strong transcription	H1 Cell Line	embryonic stem cell
8	chr15:41140200-41149600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr15:41140200-41149800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr15:41140200-41150000	Weak transcription	Rectal Smooth Muscle	rectum
11	chr15:41140400-41149400	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:41140400-41151200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:41140600-41147800	Weak transcription	Primary hematopoietic stem cells	blood
14	chr15:41140600-41149400	Strong transcription	NHEK	skin
15	chr15:41140600-41150000	Weak transcription	Fetal Kidney	kidney
16	chr15:41140600-41151600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:41140800-41148600	Weak transcription	Stomach Mucosa	stomach
18	chr15:41140800-41149400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:41140800-41149600	Weak transcription	K562	blood
20	chr15:41141200-41152600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:41141400-41149000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:41141600-41149000	Strong transcription	HMEC	breast
23	chr15:41141800-41148800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
24	chr15:41141800-41149800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:41142000-41149800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:41142400-41149600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
27	chr15:41142600-41148800	Strong transcription	Monocytes-CD14+_RO01746	blood
28	chr15:41142600-41149400	Strong transcription	Lung	lung
29	chr15:41142600-41149600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:41142600-41149600	Strong transcription	Fetal Stomach	stomach
31	chr15:41143200-41149400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:41143800-41148600	Strong transcription	Gastric	stomach
33	chr15:41144000-41147200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr15:41144400-41149600	Strong transcription	Pancreas	Pancrea
35	chr15:41144600-41148600	Strong transcription	Placenta	Placenta
36	chr15:41144600-41149400	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr15:41144600-41149600	Strong transcription	Esophagus	oesophagus
38	chr15:41144800-41149400	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:41144800-41149800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr15:41145000-41149000	Strong transcription	Primary monocytes fromperipheralblood	blood
41	chr15:41145200-41149000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr15:41145200-41149200	Weak transcription	HepG2	liver
43	chr15:41145200-41149600	Strong transcription	H9 Cell Line	embryonic stem cell
44	chr15:41145400-41148400	Strong transcription	Duodenum Mucosa	Duodenum
45	chr15:41145400-41149000	Strong transcription	Placenta Amnion	Placenta Amnion
46	chr15:41145600-41148800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr15:41145600-41148800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:41145600-41149000	Strong transcription	Fetal Intestine Large	intestine
49	chr15:41145800-41147400	Strong transcription	ES-I3 Cell Line	embryonic stem cell
50	chr15:41145800-41147600	Strong transcription	Colonic Mucosa	Colon

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