Variant report

Variant	rs17672041
Chromosome Location	chr15:40722426-40722427
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40713682..40716417-chr15:40720904..40723012,2	MCF-7	breast:
2	chr15:40721609..40723938-chr15:40763922..40765689,2	K562	blood:
3	chr15:40715093..40719455-chr15:40720778..40725123,5	K562	blood:
4	chr15:40720491..40723802-chr15:40727203..40729063,3	MCF-7	breast:
5	chr15:40702365..40704196-chr15:40720889..40723343,2	K562	blood:
6	chr15:40721609..40724539-chr15:40764189..40766844,2	K562	blood:

Variant related genes	Relation type
ENSG00000128928	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11541642	1.00[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs11557072	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11858714	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12905240	1.00[JPT][hapmap]
rs16970709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs16970758	1.00[JPT][hapmap]
rs17671194	0.92[CEU][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17671250	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17733008	1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2053973	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs34088794	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs3803358	1.00[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs55788133	1.00[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs55944373	1.00[AFR][1000 genomes]
rs55982218	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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]
rs679882	0.89[CHD][hapmap];1.00[JPT][hapmap]
rs7164132	0.85[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7164321	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7166991	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169262	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7169404	0.92[CEU][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7172000	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8026523	0.92[CEU][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs8027487	1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs8033938	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8037207	0.85[EUR][1000 genomes]
rs8040755	1.00[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs8042758	1.00[JPT][hapmap]

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	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

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs17672041	KNSTRN	cis	Esophagus Muscularis	GTEx
rs17672041	KNSTRN	cis	Artery Tibial	GTEx
rs17672041	IVD	cis	cerebellum	SCAN
rs17672041	KNSTRN	cis	Skin Sun Exposed Lower leg	GTEx
rs17672041	C15orf23	cis	multi-tissue	Pritchard
rs17672041	IVD	cis	Thyroid	GTEx
rs17672041	IVD	cis	Esophagus Mucosa	GTEx
rs17672041	C15orf23	cis	cerebellum	SCAN
rs17672041	C15orf23	trans	brain	seeQTL
rs17672041	C15orf23	cis	parietal	SCAN
rs17672041	IVD	cis	lung	GTEx
rs17672041	IVD	cis	parietal	SCAN
rs17672041	KNSTRN	cis	Adipose Subcutaneous	GTEx
rs17672041	SPTBN5	cis	cerebellum	SCAN
rs17672041	KNSTRN	cis	Heart Left Ventricle	GTEx
rs17672041	C15orf23	cis	brain	seeQTL
rs17672041	KNSTRN	cis	Nerve Tibial	GTEx
rs17672041	KNSTRN	cis	Whole Blood	GTEx
rs17672041	IVD	cis	lymphoblastoid	seeQTL
rs17672041	FLJ14502	cis	multi-tissue	Pritchard
rs17672041	IVD	cis	multi-tissue	Pritchard
rs17672041	IVD	cis	Esophagus Muscularis	GTEx
rs17672041	KNSTRN	cis	lung	GTEx
rs17672041	KNSTRN	cis	Esophagus Mucosa	GTEx
rs17672041	KNSTRN	cis	Artery Aorta	GTEx
rs17672041	KNSTRN	cis	Muscle Skeletal	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40705600-40727200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr15:40708400-40728000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:40710800-40727000	Weak transcription	Primary T cells from cord blood	blood
4	chr15:40710800-40728000	Weak transcription	Aorta	Aorta
5	chr15:40711000-40724800	Weak transcription	Primary hematopoietic stem cells	blood
6	chr15:40711800-40726600	Weak transcription	Thymus	Thymus
7	chr15:40714200-40726800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr15:40714200-40727800	Weak transcription	Brain Angular Gyrus	brain
9	chr15:40714200-40727800	Weak transcription	Esophagus	oesophagus
10	chr15:40714200-40728000	Weak transcription	Brain Substantia Nigra	brain
11	chr15:40714200-40728000	Weak transcription	Right Ventricle	heart
12	chr15:40714400-40725000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr15:40714400-40726400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr15:40714400-40727800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:40714400-40727800	Weak transcription	Right Atrium	heart
16	chr15:40714400-40728000	Weak transcription	Brain Anterior Caudate	brain
17	chr15:40714600-40722800	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr15:40714600-40724400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr15:40717200-40723400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr15:40719600-40727600	Weak transcription	Primary B cells from peripheral blood	blood
21	chr15:40719600-40727800	Weak transcription	Spleen	Spleen
22	chr15:40719600-40728000	Weak transcription	Lung	lung
23	chr15:40719800-40725600	Weak transcription	Ovary	ovary
24	chr15:40719800-40727600	Weak transcription	Gastric	stomach
25	chr15:40720400-40722800	Weak transcription	Stomach Smooth Muscle	stomach
26	chr15:40720600-40723000	Enhancers	H1 Cell Line	embryonic stem cell
27	chr15:40720800-40723000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr15:40721400-40722600	Enhancers	HUES48 Cell Line	embryonic stem cell
29	chr15:40721400-40722600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:40721400-40722800	Enhancers	H9 Cell Line	embryonic stem cell
31	chr15:40721400-40722800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr15:40721400-40722800	Enhancers	HSMMtube	muscle
33	chr15:40721600-40724600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:40721800-40723000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
35	chr15:40722000-40722800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
36	chr15:40722200-40722600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:40722200-40722600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:40722200-40722800	Enhancers	iPS-20b Cell Line	embryonic stem cell
39	chr15:40722200-40722800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr15:40722200-40722800	Enhancers	Placenta	Placenta
41	chr15:40722200-40722800	Flanking Active TSS	K562	blood
42	chr15:40722200-40722800	Flanking Active TSS	NHDF-Ad	bronchial
43	chr15:40722200-40722800	Flanking Bivalent TSS/Enh	NHEK	skin
44	chr15:40722200-40723000	Enhancers	Adipose Nuclei	Adipose
45	chr15:40722200-40723000	Enhancers	Placenta Amnion	Placenta Amnion
46	chr15:40722200-40723400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:40722400-40722600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
48	chr15:40722400-40722600	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr15:40722400-40722600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
50	chr15:40722400-40722600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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