Variant report

Variant	rs4575496
Chromosome Location	chr15:40649590-40649591
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	MAZ	chr15:40649539-40651428	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40641840..40644016-chr15:40647605..40650269,2	K562	blood:
2	chr15:40648717..40650505-chr15:40656910..40660408,3	MCF-7	breast:
3	chr15:40646801..40650118-chr15:40732469..40735250,3	K562	blood:

Variant related genes	Relation type
DISP2	TF binding region
ENSG00000140320	Chromatin interaction
ENSG00000233041	Chromatin interaction
ENSG00000140323	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11630119	0.82[ASN][1000 genomes]
rs34230187	0.82[ASN][1000 genomes]
rs61654142	0.82[ASN][1000 genomes]
rs62017982	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62017984	0.82[ASN][1000 genomes]
rs62017985	0.82[ASN][1000 genomes]
rs72733420	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs4575496	C15orf62	cis	parietal	SCAN
rs4575496	C15orf57	cis	cerebellum	SCAN
rs4575496	INO80	cis	cerebellum	SCAN
rs4575496	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs4575496	IVD	cis	Muscle Skeletal	GTEx
rs4575496	C15orf23	cis	parietal	SCAN
rs4575496	IVD	cis	parietal	SCAN
rs4575496	IVD	cis	lymphoblastoid	seeQTL
rs4575496	C15orf57	cis	parietal	SCAN
rs4575496	C15orf23	cis	cerebellum	SCAN

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40636400-40650000	Weak transcription	Right Atrium	heart
2	chr15:40637400-40649600	Weak transcription	Spleen	Spleen
3	chr15:40641600-40649600	Weak transcription	Esophagus	oesophagus
4	chr15:40643400-40649800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:40644200-40649800	Weak transcription	Primary T cells from cord blood	blood
6	chr15:40645200-40649800	Weak transcription	Small Intestine	intestine
7	chr15:40645800-40649800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr15:40646600-40649800	Weak transcription	A549	lung
9	chr15:40646800-40649600	Genic enhancers	Fetal Intestine Large	intestine
10	chr15:40646800-40649800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:40646800-40649800	Weak transcription	Pancreas	Pancrea
12	chr15:40647000-40649600	Weak transcription	Brain Hippocampus Middle	brain
13	chr15:40647000-40649800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr15:40647000-40649800	Weak transcription	Liver	Liver
15	chr15:40647000-40649800	Weak transcription	Placenta	Placenta
16	chr15:40647000-40649800	Weak transcription	Right Ventricle	heart
17	chr15:40647000-40649800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:40647000-40649800	Weak transcription	HSMMtube	muscle
19	chr15:40647000-40649800	Weak transcription	K562	blood
20	chr15:40647000-40649800	Weak transcription	Osteobl	bone
21	chr15:40647000-40650000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr15:40647000-40650000	Weak transcription	Gastric	stomach
23	chr15:40647000-40650000	Weak transcription	Psoas Muscle	Psoas
24	chr15:40647000-40650000	Weak transcription	HSMM	muscle
25	chr15:40647200-40649600	Weak transcription	Brain Germinal Matrix	brain
26	chr15:40647200-40649600	Weak transcription	Fetal Heart	heart
27	chr15:40647200-40649600	Weak transcription	Lung	lung
28	chr15:40647200-40649800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:40647200-40649800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:40647200-40649800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr15:40647200-40649800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:40647200-40649800	Genic enhancers	Fetal Intestine Small	intestine
33	chr15:40647200-40649800	Weak transcription	Fetal Muscle Leg	muscle
34	chr15:40647200-40649800	Weak transcription	Fetal Stomach	stomach
35	chr15:40647200-40649800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr15:40647200-40649800	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr15:40647200-40649800	Weak transcription	NH-A	brain
38	chr15:40647200-40650000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr15:40647400-40649600	Weak transcription	Cortex derived primary cultured neurospheres	brain
40	chr15:40647400-40649600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:40647400-40649800	Weak transcription	Brain Angular Gyrus	brain
42	chr15:40647400-40650000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr15:40647400-40650000	Weak transcription	Brain Substantia Nigra	brain
44	chr15:40647600-40649600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr15:40647800-40649800	Weak transcription	NHDF-Ad	bronchial
46	chr15:40648200-40650000	Weak transcription	Left Ventricle	heart
47	chr15:40648800-40649800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr15:40648800-40651400	Enhancers	Stomach Mucosa	stomach
49	chr15:40649000-40649600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
50	chr15:40649000-40649800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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