Variant report

Variant	rs17674454
Chromosome Location	chr15:40889824-40889825
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:40888439..40890299-chr15:40942541..40945027,2	K562	blood:
2	chr15:40884637..40889853-chr15:40895293..40899936,6	K562	blood:

Variant related genes	Relation type
ENSG00000238559	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 26 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10152546	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1044474	0.96[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs10518697	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1058734	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes]
rs11070283	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11630273	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11633184	0.92[EUR][1000 genomes]
rs11637245	0.89[EUR][1000 genomes]
rs11637422	0.91[EUR][1000 genomes]
rs12148915	0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs12324748	0.92[EUR][1000 genomes]
rs12385982	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12441754	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12591044	0.80[AMR][1000 genomes]
rs12592524	0.92[CEU][hapmap];1.00[JPT][hapmap]
rs12903817	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12907442	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12908316	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12913296	0.89[EUR][1000 genomes]
rs12913739	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12915171	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12915636	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13329076	0.84[EUR][1000 genomes]
rs17673703	1.00[CEU][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs17747423	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17747633	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1801321	0.92[CEU][hapmap];0.80[AMR][1000 genomes]
rs1814541	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1814542	0.81[EUR][1000 genomes]
rs2412525	0.92[EUR][1000 genomes]
rs28529389	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs28634695	0.89[EUR][1000 genomes]
rs28647196	0.82[EUR][1000 genomes]
rs28669075	0.89[EUR][1000 genomes]
rs28891195	0.81[AMR][1000 genomes]
rs34739056	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34824658	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35127391	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35684277	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35842610	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4923880	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4924486	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4924496	0.92[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs4924502	0.80[AMR][1000 genomes]
rs62019876	0.92[EUR][1000 genomes]
rs62019879	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6492964	0.85[CEU][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap]
rs71471880	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7165509	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7170288	0.91[EUR][1000 genomes]
rs7175747	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176245	0.80[AMR][1000 genomes]
rs7176590	0.82[AMR][1000 genomes]
rs7177265	0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap];0.80[AMR][1000 genomes]
rs7180135	0.92[CEU][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes]
rs7182499	0.82[AMR][1000 genomes]
rs8029530	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8036891	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8037180	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8038122	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8042386	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs957603	0.92[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs9920642	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9920676	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv832984	chr15:40794391-40998535	Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	esv2758378	chr15:40832545-40995111	Active TSS Flanking Active TSS Strong transcription Enhancers Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2760026	chr15:40832545-40995111	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:26)

SNP	Gene	Cis/trans	Tissue	Source
rs17674454	C15orf57	cis	Nerve Tibial	GTEx
rs17674454	CCDC32	cis	multi-tissue	Pritchard
rs17674454	C15orf57	cis	Skin Sun Exposed Lower leg	GTEx
rs17674454	CCDC32	cis	normal skin	skin_eQTL
rs17674454	RP11-111A22.1	cis	Adipose Subcutaneous	GTEx
rs17674454	C15orf57	cis	cerebellum	SCAN
rs17674454	C15orf57	cis	Artery Tibial	GTEx
rs17674454	C15orf57	cis	parietal	SCAN
rs17674454	C15orf57	cis	Artery Aorta	GTEx
rs17674454	C15orf57	cis	Heart Left Ventricle	GTEx
rs17674454	C15orf57	cis	Adipose Subcutaneous	GTEx
rs17674454	C15orf57	cis	Stomach	GTEx
rs17674454	RP11-111A22.1	cis	Heart Left Ventricle	GTEx
rs17674454	RP11-111A22.1	cis	Artery Tibial	GTEx
rs17674454	MAPKBP1	cis	cerebellum	SCAN
rs17674454	C15orf57	cis	Esophagus Muscularis	GTEx
rs17674454	C15orf57	cis	Esophagus Mucosa	GTEx
rs17674454	MRPL42P5	cis	lymphoblastoid	seeQTL
rs17674454	MRPL42P5	cis	multi-tissue	Pritchard
rs17674454	RP11-111A22.1	cis	lung	GTEx
rs17674454	C15orf57	cis	lung	GTEx
rs17674454	RAD51	cis	multi-tissue	Pritchard
rs17674454	CCDC32	cis	lesional skin	skin_eQTL
rs17674454	CCDC32	cis	uninvolved skin	skin_eQTL
rs17674454	C15orf57	cis	Muscle Skeletal	GTEx
rs17674454	RP11-111A22.1	cis	Artery Aorta	GTEx

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40887200-40893200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:40887200-40898800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr15:40887400-40891600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr15:40887600-40898800	Weak transcription	Fetal Muscle Trunk	muscle
5	chr15:40887600-40902600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40887600-40941800	Weak transcription	Fetal Intestine Large	intestine
7	chr15:40887800-40895400	Weak transcription	Fetal Muscle Leg	muscle
8	chr15:40887800-40898800	Weak transcription	Fetal Stomach	stomach
9	chr15:40887800-40902000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr15:40887800-40933200	Weak transcription	Duodenum Mucosa	Duodenum
11	chr15:40887800-40942200	Weak transcription	Primary B cells from cord blood	blood
12	chr15:40887800-40948200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr15:40887800-40961600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:40888000-40892800	Weak transcription	Fetal Heart	heart
15	chr15:40888000-40895000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr15:40888000-40895800	Weak transcription	Thymus	Thymus
17	chr15:40888000-40897800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr15:40888000-40898000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr15:40888000-40898600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:40888000-40899400	Weak transcription	HSMM	muscle
21	chr15:40888000-40901200	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr15:40888000-40903400	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr15:40888000-40956000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr15:40888200-40890400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr15:40888200-40890400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:40888200-40890400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr15:40888200-40897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:40888200-40898600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr15:40888200-40898800	Weak transcription	NH-A	brain
30	chr15:40888200-40902200	Weak transcription	HUES6 Cell Line	embryonic stem cell
31	chr15:40888200-40912800	Weak transcription	HMEC	breast
32	chr15:40888400-40890200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:40888400-40890400	Weak transcription	NHEK	skin
34	chr15:40888400-40892800	Weak transcription	Brain Germinal Matrix	brain
35	chr15:40888400-40895800	Weak transcription	Fetal Thymus	thymus
36	chr15:40888400-40897800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:40888400-40898000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr15:40888400-40898200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:40888400-40898800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
40	chr15:40888400-40898800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr15:40888400-40898800	Weak transcription	Fetal Intestine Small	intestine
42	chr15:40888400-40899800	Weak transcription	HUVEC	blood vessel
43	chr15:40888400-40900800	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr15:40888400-40913200	Weak transcription	NHDF-Ad	bronchial
45	chr15:40888400-40913600	Weak transcription	NHLF	lung
46	chr15:40888400-40923200	Weak transcription	Osteobl	bone
47	chr15:40888400-40925800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
48	chr15:40888400-40944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:40889200-40890400	Genic enhancers	Dnd41	blood
50	chr15:40889400-40890000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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