Variant report

Variant	rs17671250
Chromosome Location	chr15:40673124-40673125
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:40649433..40650953-chr15:40671717..40674000,2	K562	blood:
2	chr15:40671643..40673805-chr15:40689651..40692222,2	K562	blood:
3	chr15:40670502..40673143-chr15:40690722..40692887,2	K562	blood:

Variant related genes	Relation type
ENSG00000140323	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 28 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11541642	0.90[EUR][1000 genomes]
rs11557072	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11858714	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12905240	1.00[JPT][hapmap]
rs16970709	1.00[JPT][hapmap]
rs16970758	1.00[JPT][hapmap]
rs17671194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17672041	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[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2053973	1.00[JPT][hapmap]
rs34088794	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3803358	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55788133	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55982218	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58467866	0.81[AFR][1000 genomes]
rs61298638	0.83[AFR][1000 genomes]
rs679882	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164132	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164321	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169262	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169404	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7172000	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73383108	0.85[AFR][1000 genomes]
rs8026523	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8027487	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8033303	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8033668	0.85[AFR][1000 genomes]
rs8033938	1.00[CEU][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8037207	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8040755	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8041293	0.87[YRI][hapmap];0.88[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:28)

SNP	Gene	Cis/trans	Tissue	Source
rs17671250	KNSTRN	cis	Esophagus Muscularis	GTEx
rs17671250	SPTBN5	cis	cerebellum	SCAN
rs17671250	FLJ14502	cis	multi-tissue	Pritchard
rs17671250	KNSTRN	cis	Whole Blood	GTEx
rs17671250	C15orf23	cis	brain	seeQTL
rs17671250	C15orf23	trans	brain	seeQTL
rs17671250	IVD	cis	parietal	SCAN
rs17671250	KNSTRN	cis	Esophagus Mucosa	GTEx
rs17671250	KNSTRN	cis	Artery Aorta	GTEx
rs17671250	KNSTRN	cis	lung	GTEx
rs17671250	C15orf23	cis	multi-tissue	Pritchard
rs17671250	IVD	cis	multi-tissue	Pritchard
rs17671250	KNSTRN	cis	Nerve Tibial	GTEx
rs17671250	IVD	cis	Thyroid	GTEx
rs17671250	KNSTRN	cis	Artery Tibial	GTEx
rs17671250	IVD	cis	Artery Tibial	GTEx
rs17671250	IVD	cis	Esophagus Muscularis	GTEx
rs17671250	C15orf23	cis	parietal	SCAN
rs17671250	STOM	trans	parietal	SCAN
rs17671250	KNSTRN	cis	Muscle Skeletal	GTEx
rs17671250	KNSTRN	cis	Heart Left Ventricle	GTEx
rs17671250	IVD	cis	cerebellum	SCAN
rs17671250	LPCAT4	cis	parietal	SCAN
rs17671250	C15orf23	cis	cerebellum	SCAN
rs17671250	C15orf23	cis	Liver	GTEx
rs17671250	IVD	cis	lung	GTEx
rs17671250	KNSTRN	cis	Skin Sun Exposed Lower leg	GTEx
rs17671250	KNSTRN	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40660800-40674800	Weak transcription	Esophagus	oesophagus
2	chr15:40661200-40674800	Weak transcription	Fetal Brain Male	brain
3	chr15:40661600-40674600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:40663200-40674800	Weak transcription	Brain Germinal Matrix	brain
5	chr15:40663800-40674200	Weak transcription	Right Ventricle	heart
6	chr15:40665200-40674800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:40665200-40674800	Weak transcription	Fetal Brain Female	brain
8	chr15:40665400-40674800	Weak transcription	Fetal Lung	lung
9	chr15:40668000-40674600	Weak transcription	Thymus	Thymus
10	chr15:40670000-40674800	Weak transcription	Aorta	Aorta
11	chr15:40671400-40673200	Enhancers	HSMMtube	muscle
12	chr15:40671400-40673200	Enhancers	NHDF-Ad	bronchial
13	chr15:40671400-40673400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr15:40671600-40673200	Enhancers	NHEK	skin
15	chr15:40671600-40674200	Weak transcription	Lung	lung
16	chr15:40671600-40674800	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:40671800-40673200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
18	chr15:40671800-40673200	Enhancers	HMEC	breast
19	chr15:40671800-40674800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:40671800-40674800	Weak transcription	Psoas Muscle	Psoas
21	chr15:40672200-40673800	Weak transcription	Liver	Liver
22	chr15:40672200-40674200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
23	chr15:40672200-40674800	Weak transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:40672200-40674800	Weak transcription	Left Ventricle	heart
25	chr15:40672400-40673800	Weak transcription	HepG2	liver
26	chr15:40672400-40674400	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr15:40672400-40674800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:40672400-40674800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:40672400-40674800	Weak transcription	Cortex derived primary cultured neurospheres	brain
30	chr15:40672400-40674800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:40672400-40674800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:40672400-40674800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr15:40672400-40674800	Weak transcription	Gastric	stomach
34	chr15:40672400-40674800	Weak transcription	Spleen	Spleen
35	chr15:40672600-40673200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:40672600-40673200	Enhancers	Muscle Satellite Cultured Cells	--
37	chr15:40672600-40673200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:40672600-40673200	Enhancers	Hela-S3	cervix
39	chr15:40672600-40674000	Weak transcription	A549	lung
40	chr15:40672600-40674000	Weak transcription	K562	blood
41	chr15:40672600-40674600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr15:40672600-40674600	Weak transcription	Adipose Nuclei	Adipose
43	chr15:40672600-40674600	Weak transcription	Brain Cingulate Gyrus	brain
44	chr15:40672600-40674600	Weak transcription	Fetal Heart	heart
45	chr15:40672600-40674600	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr15:40672600-40674600	Weak transcription	Osteobl	bone
47	chr15:40672600-40674800	Weak transcription	Primary monocytes fromperipheralblood	blood
48	chr15:40672600-40674800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:40672600-40674800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:40672600-40674800	Weak transcription	Sigmoid Colon	Sigmoid Colon

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