Variant report

Variant	rs11557072
Chromosome Location	chr15:40713374-40713375
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40704069..40706922-chr15:40710416..40713548,3	MCF-7	breast:
2	chr15:40705175..40706688-chr15:40711087..40713954,2	MCF-7	breast:
3	chr15:40659557..40661965-chr15:40712897..40715534,3	MCF-7	breast:
4	chr15:40706979..40709037-chr15:40711675..40714916,3	MCF-7	breast:
5	chr15:40708302..40709831-chr15:40711317..40714236,2	MCF-7	breast:
6	chr15:40571973..40573796-chr15:40712353..40713860,2	K562	blood:
7	chr15:40614961..40616867-chr15:40712396..40714190,2	MCF-7	breast:
8	chr15:40709951..40712517-chr15:40713358..40716210,2	K562	blood:
9	chr15:40660254..40663896-chr15:40712665..40714406,3	MCF-7	breast:
10	chr15:40712357..40714224-chr15:40720673..40722209,2	MCF-7	breast:
11	chr15:40662906..40663770-chr15:40713312..40714091,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000140323	Chromatin interaction
ENSG00000128928	Chromatin interaction
ENSG00000259368	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11541642	1.00[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs11858714	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17671194	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17671250	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17672041	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17733008	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34088794	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3803358	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55788133	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs55944373	1.00[AFR][1000 genomes]
rs55982218	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044352	1.00[AFR][1000 genomes]
rs56190115	1.00[AFR][1000 genomes]
rs56334337	1.00[AFR][1000 genomes]
rs7164132	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164321	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166991	1.00[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169262	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169404	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172000	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026523	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs8027487	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8033938	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037207	0.86[EUR][1000 genomes]
rs8040755	1.00[AFR][1000 genomes];0.86[EUR][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:18)

SNP	Gene	Cis/trans	Tissue	Source
rs11557072	KNSTRN	cis	Artery Tibial	GTEx
rs11557072	C15orf23	cis	multi-tissue	Pritchard
rs11557072	KNSTRN	cis	Esophagus Muscularis	GTEx
rs11557072	KNSTRN	cis	Artery Aorta	GTEx
rs11557072	KNSTRN	cis	lung	GTEx
rs11557072	C15orf23	Cis_1M	lymphoblastoid	RTeQTL
rs11557072	KNSTRN	cis	Whole Blood	GTEx
rs11557072	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs11557072	IVD	cis	lung	GTEx
rs11557072	IVD	cis	Thyroid	GTEx
rs11557072	KNSTRN	cis	Skin Sun Exposed Lower leg	GTEx
rs11557072	IVD	cis	Esophagus Mucosa	GTEx
rs11557072	KNSTRN	cis	Heart Left Ventricle	GTEx
rs11557072	IVD	cis	Esophagus Muscularis	GTEx
rs11557072	KNSTRN	cis	Nerve Tibial	GTEx
rs11557072	KNSTRN	cis	Esophagus Mucosa	GTEx
rs11557072	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs11557072	KNSTRN	cis	Muscle Skeletal	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40699000-40714000	Weak transcription	Small Intestine	intestine
2	chr15:40699600-40714000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:40704200-40713800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:40704400-40714000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr15:40705600-40727200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr15:40708200-40713800	Weak transcription	Primary B cells from cord blood	blood
7	chr15:40708400-40713600	Weak transcription	NHDF-Ad	bronchial
8	chr15:40708400-40714000	Weak transcription	Fetal Brain Male	brain
9	chr15:40708400-40721200	Weak transcription	Fetal Kidney	kidney
10	chr15:40708400-40728000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:40708600-40713800	Weak transcription	GM12878-XiMat	blood
12	chr15:40708600-40714000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr15:40708600-40714000	Weak transcription	A549	lung
14	chr15:40709000-40714000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr15:40710000-40718600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr15:40710400-40713800	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr15:40710600-40713600	Weak transcription	Brain Angular Gyrus	brain
18	chr15:40710800-40713600	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:40710800-40713800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr15:40710800-40714000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:40710800-40714000	Weak transcription	NHLF	lung
22	chr15:40710800-40727000	Weak transcription	Primary T cells from cord blood	blood
23	chr15:40710800-40728000	Weak transcription	Aorta	Aorta
24	chr15:40711000-40713400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:40711000-40713400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr15:40711000-40713600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr15:40711000-40713600	Weak transcription	Primary T cells fromperipheralblood	blood
28	chr15:40711000-40713600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:40711000-40713600	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr15:40711000-40713600	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr15:40711000-40713600	Weak transcription	Colonic Mucosa	Colon
32	chr15:40711000-40713600	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:40711000-40713600	Weak transcription	Fetal Intestine Large	intestine
34	chr15:40711000-40713600	Weak transcription	HepG2	liver
35	chr15:40711000-40713800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr15:40711000-40713800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr15:40711000-40713800	Weak transcription	Brain Germinal Matrix	brain
38	chr15:40711000-40714000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr15:40711000-40714000	Weak transcription	Brain Anterior Caudate	brain
40	chr15:40711000-40714000	Weak transcription	Brain Hippocampus Middle	brain
41	chr15:40711000-40714000	Weak transcription	Dnd41	blood
42	chr15:40711000-40719400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr15:40711000-40721400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr15:40711000-40722000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:40711000-40724800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr15:40711200-40713400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:40711200-40713800	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr15:40711200-40713800	Weak transcription	Primary B cells from peripheral blood	blood
49	chr15:40711200-40714000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr15:40711400-40713400	Weak transcription	Cortex derived primary cultured neurospheres	brain

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