Variant report

Variant	rs8041458
Chromosome Location	chr15:42196846-42196847
allele	C/G
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:42064627..42065588-chr15:42196454..42197410,5	K562	blood:
2	chr15:42194241..42196970-chr15:42258249..42260328,2	K562	blood:
3	chr15:42115008..42115577-chr15:42196451..42197341,2	MCF-7	breast:
4	chr15:42196472..42197471-chr15:42376282..42376802,2	K562	blood:
5	chr15:42176708..42178291-chr15:42195146..42197616,2	K562	blood:
6	chr15:42184791..42187118-chr15:42195366..42196977,2	K562	blood:
7	chr15:42184589..42187118-chr15:42195366..42198157,2	K562	blood:
8	chr15:42066376..42067229-chr15:42196456..42197004,2	K562	blood:
9	chr15:41895978..41896965-chr15:42196438..42197404,2	MCF-7	breast:
10	chr15:42114988..42115997-chr15:42196197..42197506,6	MCF-7	breast:
11	chr15:42170088..42170778-chr15:42196301..42197330,4	K562	blood:
12	chr15:42180442..42182824-chr15:42195792..42198246,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000174171	Chromatin interaction
ENSG00000137802	Chromatin interaction
ENSG00000137877	Chromatin interaction
ENSG00000260814	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1048166	0.82[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap]
rs1048175	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs10518741	1.00[CHB][hapmap];0.91[CHD][hapmap];0.80[MEX][hapmap];0.86[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11070353	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11636960	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1197691	1.00[CHB][hapmap]
rs1209334	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.80[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13329244	0.82[CHB][hapmap]
rs1648815	0.80[ASN][1000 genomes]
rs1648818	0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1672461	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1704386	0.80[ASN][1000 genomes]
rs1704388	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1704389	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1704391	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs1704392	0.82[CEU][hapmap]
rs1704396	0.80[CEU][hapmap];0.85[CHB][hapmap];0.83[CHD][hapmap];0.80[ASN][1000 genomes]
rs17686769	0.82[CHB][hapmap];1.00[CHD][hapmap]
rs2271283	0.82[CHB][hapmap]
rs28547280	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28550631	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7166358	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7172468	0.88[EUR][1000 genomes]
rs7183264	0.90[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs890502	0.85[CEU][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs9920696	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv427958	chr15:42051317-42301283	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv904116	chr15:42076387-42229852	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	25 gene(s)	inside rSNPs	diseases
4	esv1827003	chr15:42087505-42199076	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1035998	chr15:42098896-42434254	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	38 gene(s)	inside rSNPs	diseases
6	nsv904118	chr15:42103822-42207905	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	nsv904124	chr15:42109975-42207905	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
8	nsv9244	chr15:42110712-42208805	Enhancers Genic enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
9	nsv904125	chr15:42119900-42210393	Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Enhancers Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	19 gene(s)	inside rSNPs	diseases
10	nsv1038933	chr15:42138456-42309087	Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	30 gene(s)	inside rSNPs	diseases
11	nsv904127	chr15:42142912-42207905	Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
12	nsv904128	chr15:42147639-42207905	Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
13	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
14	nsv904129	chr15:42162957-42207905	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
15	nsv1054728	chr15:42177772-42310009	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs8041458	SPTBN5	cis	Esophagus Muscularis	GTEx
rs8041458	SPTBN5	cis	Artery Tibial	GTEx
rs8041458	SPTBN5	cis	multi-tissue	Pritchard
rs8041458	NDUFAF1	cis	parietal	SCAN
rs8041458	SPTBN5	cis	cerebellum	SCAN
rs8041458	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs8041458	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs8041458	EHD4	cis	multi-tissue	Pritchard
rs8041458	SPTBN5	cis	Artery Aorta	GTEx
rs8041458	C15orf23	cis	cerebellum	SCAN
rs8041458	SPTBN5	cis	Thyroid	GTEx
rs8041458	SPTBN5	cis	Whole Blood	GTEx
rs8041458	MAPKBP1	cis	cerebellum	SCAN
rs8041458	RPAP1	cis	parietal	SCAN
rs8041458	SPTBN5	cis	Muscle Skeletal	GTEx
rs8041458	C15orf23	cis	parietal	SCAN
rs8041458	SPTBN5	cis	lung	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42186800-42198800	Weak transcription	Brain Substantia Nigra	brain
2	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
3	chr15:42187600-42198800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr15:42187600-42200400	Weak transcription	Stomach Mucosa	stomach
5	chr15:42187600-42200600	Weak transcription	HepG2	liver
6	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
7	chr15:42187800-42198000	Strong transcription	Fetal Intestine Small	intestine
8	chr15:42187800-42206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr15:42188000-42197000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
10	chr15:42188000-42198600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr15:42188000-42198800	Weak transcription	Primary hematopoietic stem cells	blood
12	chr15:42188400-42197000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:42188400-42197000	Strong transcription	Lung	lung
14	chr15:42188600-42209600	Strong transcription	NHEK	skin
15	chr15:42189000-42198200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr15:42189200-42197400	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr15:42189400-42198800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:42189800-42208400	Strong transcription	HUVEC	blood vessel
19	chr15:42190000-42197000	Weak transcription	Fetal Thymus	thymus
20	chr15:42190200-42209800	Weak transcription	Hela-S3	cervix
21	chr15:42190400-42218600	Weak transcription	Fetal Lung	lung
22	chr15:42191600-42197000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr15:42191600-42197200	Weak transcription	Primary B cells from cord blood	blood
24	chr15:42191600-42198600	Weak transcription	Osteobl	bone
25	chr15:42192200-42198000	Enhancers	Fetal Heart	heart
26	chr15:42192400-42198600	Weak transcription	Ovary	ovary
27	chr15:42192600-42197800	Weak transcription	Primary T cells from cord blood	blood
28	chr15:42192600-42204000	Strong transcription	Esophagus	oesophagus
29	chr15:42193200-42198200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:42193200-42199000	Weak transcription	NH-A	brain
31	chr15:42193400-42197000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:42193400-42198600	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr15:42193400-42200600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr15:42193600-42197000	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr15:42193600-42198000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
36	chr15:42193600-42198200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:42193600-42198200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr15:42193600-42198400	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:42193600-42198600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr15:42193600-42200600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:42193800-42197000	Weak transcription	Fetal Intestine Large	intestine
42	chr15:42193800-42197200	Weak transcription	Aorta	Aorta
43	chr15:42193800-42198000	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr15:42193800-42198600	Weak transcription	Primary T helper cells PMA-I stimulated	--
45	chr15:42193800-42198600	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:42194200-42198800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
47	chr15:42194400-42197000	Weak transcription	Spleen	Spleen
48	chr15:42194400-42198200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:42194400-42198200	Weak transcription	Rectal Mucosa Donor 29	rectum
50	chr15:42194400-42198200	Weak transcription	Rectal Mucosa Donor 31	rectum

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