Variant report

Variant	rs1048175
Chromosome Location	chr15:42191909-42191910
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:42191716-42191987	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:42191107-42191965	GM12892	blood:	n/a	n/a
3	POLR2A	chr15:42191654-42192681	GM12891	blood:	n/a	n/a
4	POLR2A	chr15:42191848-42192418	GM12892	blood:	n/a	n/a
5	POLR2A	chr15:42191518-42192026	HUVEC	blood vessel:	n/a	n/a
6	POLR2A	chr15:42191691-42192346	GM12891	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:42190524..42192250-chr15:42192419..42194195,2	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-JMJD7-PLA2G4B-2	chr15:42190708-42192352	NONHSAT041985
2	lnc-SPTBN5-4	chr15:42191630-42192208	NONHSAT041986

No data

Variant related genes	Relation type
ENSG00000272003	TF binding region

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1048166	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10518741	0.85[CHB][hapmap]
rs1113333	0.82[CEU][hapmap]
rs1124850	0.82[CEU][hapmap]
rs1197691	0.85[CHB][hapmap]
rs1209334	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1648810	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648811	0.86[YRI][hapmap]
rs1648815	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1672461	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1704381	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1704386	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704388	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1704392	1.00[CEU][hapmap];0.84[CHB][hapmap]
rs1704396	0.96[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1820506	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6493011	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7183264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8041458	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[JPT][hapmap]
rs890502	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9920406	0.85[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:16 , 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	nsv1048606	chr15:42101694-42192760	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1048175	SPTBN5	cis	Artery Tibial	GTEx
rs1048175	SPTBN5	cis	Artery Aorta	GTEx
rs1048175	EHD4	Cis_1M	lymphoblastoid	RTeQTL
rs1048175	SPTBN5	cis	Adipose Subcutaneous	GTEx
rs1048175	SPTBN5	cis	Esophagus Muscularis	GTEx
rs1048175	SPTBN5	cis	lung	GTEx

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42183600-42195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:42183600-42196000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:42183800-42195800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42184400-42192800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:42186200-42192800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:42186800-42198800	Weak transcription	Brain Substantia Nigra	brain
7	chr15:42187200-42211800	Weak transcription	Small Intestine	intestine
8	chr15:42187400-42196600	Weak transcription	Brain Cingulate Gyrus	brain
9	chr15:42187600-42192000	Weak transcription	Ovary	ovary
10	chr15:42187600-42192400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:42187600-42192600	Weak transcription	Colonic Mucosa	Colon
12	chr15:42187600-42192600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:42187600-42192600	Weak transcription	Esophagus	oesophagus
14	chr15:42187600-42192800	Weak transcription	Gastric	stomach
15	chr15:42187600-42192800	Weak transcription	Right Atrium	heart
16	chr15:42187600-42196400	Weak transcription	Brain Hippocampus Middle	brain
17	chr15:42187600-42196600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:42187600-42196600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:42187600-42198800	Weak transcription	Rectal Smooth Muscle	rectum
20	chr15:42187600-42200400	Weak transcription	Stomach Mucosa	stomach
21	chr15:42187600-42200600	Weak transcription	HepG2	liver
22	chr15:42187600-42209800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:42187800-42192000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr15:42187800-42192200	Weak transcription	Stomach Smooth Muscle	stomach
25	chr15:42187800-42196200	Weak transcription	Brain Angular Gyrus	brain
26	chr15:42187800-42196400	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr15:42187800-42196600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr15:42187800-42198000	Strong transcription	Fetal Intestine Small	intestine
29	chr15:42187800-42206800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr15:42188000-42192000	Weak transcription	Fetal Heart	heart
31	chr15:42188000-42196000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:42188000-42197000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:42188000-42198600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:42188000-42198800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:42188200-42192000	Strong transcription	Fetal Muscle Trunk	muscle
36	chr15:42188400-42195800	Strong transcription	Fetal Muscle Leg	muscle
37	chr15:42188400-42197000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr15:42188400-42197000	Strong transcription	Lung	lung
39	chr15:42188600-42193200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr15:42188600-42196600	Weak transcription	Primary B cells from peripheral blood	blood
41	chr15:42188600-42209600	Strong transcription	NHEK	skin
42	chr15:42188800-42192800	Weak transcription	H9 Cell Line	embryonic stem cell
43	chr15:42188800-42193000	Strong transcription	Right Ventricle	heart
44	chr15:42188800-42193400	Strong transcription	Placenta Amnion	Placenta Amnion
45	chr15:42188800-42194600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr15:42188800-42194600	Strong transcription	HMEC	breast
47	chr15:42188800-42194800	Strong transcription	Adipose Nuclei	Adipose
48	chr15:42188800-42195800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:42189000-42195400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr15:42189000-42196400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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