Variant report

Variant	rs56190115
Chromosome Location	chr15:40645893-40645894
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40636615..40640420-chr15:40645186..40649108,5	K562	blood:
2	chr15:40641219..40644048-chr15:40645169..40646787,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHGR1-3	chr15:40645433-40645973	NONHSAT041831

Variant related genes	Relation type
ENSG00000233041	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs11541642	1.00[AFR][1000 genomes]
rs11557072	1.00[AFR][1000 genomes]
rs11858714	1.00[AFR][1000 genomes]
rs17671194	1.00[AFR][1000 genomes]
rs17672041	1.00[AFR][1000 genomes]
rs17733008	1.00[AFR][1000 genomes]
rs34088794	1.00[AFR][1000 genomes]
rs3803358	1.00[AFR][1000 genomes]
rs55788133	1.00[AFR][1000 genomes]
rs55944373	1.00[AFR][1000 genomes]
rs55982218	1.00[AFR][1000 genomes]
rs56044352	1.00[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs56334337	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164132	1.00[AFR][1000 genomes]
rs7164321	1.00[AFR][1000 genomes]
rs7166991	1.00[AFR][1000 genomes]
rs7169262	1.00[AFR][1000 genomes]
rs7169404	1.00[AFR][1000 genomes]
rs8026523	1.00[AFR][1000 genomes]
rs8027487	1.00[AFR][1000 genomes]
rs8040755	1.00[AFR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs56190115	KNSTRN	cis	Heart Left Ventricle	GTEx
rs56190115	KNSTRN	cis	Whole Blood	GTEx
rs56190115	KNSTRN	cis	Artery Tibial	GTEx
rs56190115	KNSTRN	cis	Muscle Skeletal	GTEx
rs56190115	KNSTRN	cis	Esophagus Muscularis	GTEx
rs56190115	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs56190115	KNSTRN	cis	Nerve Tibial	GTEx
rs56190115	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs56190115	KNSTRN	cis	Artery Aorta	GTEx

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40636400-40650000	Weak transcription	Right Atrium	heart
2	chr15:40636800-40646200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr15:40637400-40649600	Weak transcription	Spleen	Spleen
4	chr15:40641400-40646200	Weak transcription	Fetal Heart	heart
5	chr15:40641600-40649600	Weak transcription	Esophagus	oesophagus
6	chr15:40642400-40647000	Active TSS	Rectal Smooth Muscle	rectum
7	chr15:40643000-40646200	Active TSS	Duodenum Mucosa	Duodenum
8	chr15:40643400-40646400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr15:40643400-40649800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:40644200-40647200	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine
11	chr15:40644200-40649800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:40644600-40646000	Transcr. at gene 5' and 3'	Sigmoid Colon	Sigmoid Colon
13	chr15:40644600-40647000	Transcr. at gene 5' and 3'	Colonic Mucosa	Colon
14	chr15:40644600-40647200	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 31	rectum
15	chr15:40644600-40647600	Transcr. at gene 5' and 3'	Rectal Mucosa Donor 29	rectum
16	chr15:40644600-40648800	Enhancers	Fetal Brain Male	brain
17	chr15:40644800-40646000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr15:40644800-40647000	Enhancers	Liver	Liver
19	chr15:40644800-40647600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:40645000-40646200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr15:40645000-40646200	Weak transcription	Gastric	stomach
22	chr15:40645200-40646200	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr15:40645200-40649800	Weak transcription	Small Intestine	intestine
24	chr15:40645400-40646200	Flanking Active TSS	Fetal Intestine Large	intestine
25	chr15:40645400-40647200	Enhancers	Brain Germinal Matrix	brain
26	chr15:40645400-40647200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr15:40645400-40647200	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr15:40645400-40647200	Enhancers	Stomach Mucosa	stomach
29	chr15:40645400-40648400	Enhancers	Fetal Brain Female	brain
30	chr15:40645600-40646600	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr15:40645600-40647000	Enhancers	Brain Hippocampus Middle	brain
32	chr15:40645600-40647000	Bivalent Enhancer	Fetal Stomach	stomach
33	chr15:40645600-40647400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:40645600-40647400	Enhancers	Brain Angular Gyrus	brain
35	chr15:40645600-40649400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:40645800-40646000	Bivalent Enhancer	Placenta	Placenta
37	chr15:40645800-40646000	Bivalent Enhancer	HepG2	liver
38	chr15:40645800-40646200	Bivalent Enhancer	Fetal Muscle Leg	muscle
39	chr15:40645800-40647000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:40645800-40647000	Enhancers	Adipose Nuclei	Adipose
41	chr15:40645800-40647000	Enhancers	Psoas Muscle	Psoas
42	chr15:40645800-40647000	Enhancers	Right Ventricle	heart
43	chr15:40645800-40647000	Enhancers	HSMM	muscle
44	chr15:40645800-40647000	Enhancers	K562	blood
45	chr15:40645800-40647200	Bivalent Enhancer	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr15:40645800-40647400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:40645800-40647400	Enhancers	Brain Cingulate Gyrus	brain
48	chr15:40645800-40647400	Enhancers	Brain Substantia Nigra	brain
49	chr15:40645800-40647400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr15:40645800-40647600	Enhancers	H1 Cell Line	embryonic stem cell

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