Variant report

Variant	rs58747679
Chromosome Location	chr12:26348304-26348305
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:53)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:53 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr12:26348251-26349186	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr12:26348118-26349210	H1-hESC	embryonic stem cell:	n/a	n/a
3	USF1	chr12:26348284-26348528	SK-N-SH_RA	brain:	n/a	chr12:26348369-26348385 chr12:26348431-26348447
4	YY1	chr12:26348302-26349112	H1-hESC	embryonic stem cell:	n/a	chr12:26349050-26349061
5	TEAD4	chr12:26348218-26349189	ECC-1	luminal epithelium:	n/a	n/a
6	POLR2A	chr12:26348177-26349165	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr12:26348272-26349107	ECC-1	luminal epithelium:	n/a	n/a
8	YY1	chr12:26348165-26349179	SK-N-SH_RA	brain:	n/a	chr12:26349050-26349061
9	RAD21	chr12:26348201-26348543	SK-N-SH_RA	brain:	n/a	chr12:26348431-26348444
10	CTCF	chr12:26348240-26348390	HUVEC	blood vessel:	n/a	n/a
11	RAD21	chr12:26348290-26348550	SK-N-SH_RA	brain:	n/a	chr12:26348431-26348444
12	YY1	chr12:26348186-26349216	ECC-1	luminal epithelium:	n/a	chr12:26349050-26349061
13	POLR2A	chr12:26348171-26348886	H1-neurons	neurons:	n/a	n/a
14	TCF12	chr12:26348054-26349287	ECC-1	luminal epithelium:	n/a	n/a
15	ESR1	chr12:26348205-26348698	ECC-1	luminal epithelium:	n/a	n/a
16	MAX	chr12:26348038-26349295	ECC-1	luminal epithelium:	n/a	n/a
17	YY1	chr12:26348227-26349162	ECC-1	luminal epithelium:	n/a	chr12:26349050-26349061
18	POLR2A	chr12:26348021-26349638	PANC-1	pancreas:	n/a	n/a
19	ESR1	chr12:26348265-26348672	ECC-1	luminal epithelium:	n/a	n/a
20	RAD21	chr12:26348038-26348570	ECC-1	luminal epithelium:	n/a	chr12:26348431-26348444
21	MAX	chr12:26348087-26349308	ECC-1	luminal epithelium:	n/a	n/a
22	MAX	chr12:26348083-26349347	SK-N-SH	brain:	n/a	n/a
23	ZBTB7A	chr12:26348098-26349207	ECC-1	luminal epithelium:	n/a	n/a
24	SRF	chr12:26348194-26348755	ECC-1	luminal epithelium:	n/a	n/a
25	CTCF	chr12:26348240-26348390	GM12875	blood:	n/a	n/a
26	E2F6	chr12:26348171-26349172	H1-hESC	embryonic stem cell:	n/a	n/a
27	TAF1	chr12:26348181-26349108	ECC-1	luminal epithelium:	n/a	n/a
28	SIN3AK20	chr12:26348030-26349281	PANC-1	pancreas:	n/a	n/a
29	NFIC	chr12:26348129-26349330	ECC-1	luminal epithelium:	n/a	chr12:26348333-26348361
30	POLR2A	chr12:26348272-26349148	MCF-7	breast:	n/a	n/a
31	SRF	chr12:26348191-26348740	ECC-1	luminal epithelium:	n/a	n/a
32	GATA3	chr12:26348130-26348497	T-47D	breast:	n/a	n/a
33	ESR1	chr12:26348261-26348668	ECC-1	luminal epithelium:	n/a	n/a
34	POLR2A	chr12:26348097-26348677	SK-N-SH	brain:	n/a	n/a
35	TAF1	chr12:26348179-26348541	SK-N-SH	brain:	n/a	n/a
36	POLR2A	chr12:26348194-26348440	H1-hESC	embryonic stem cell:	n/a	n/a
37	TAF1	chr12:26348212-26348507	H1-hESC	embryonic stem cell:	n/a	n/a
38	EP300	chr12:26348062-26349366	ECC-1	luminal epithelium:	n/a	chr12:26348178-26348192 chr12:26349095-26349111
39	FOXA1	chr12:26348276-26348596	T-47D	breast:	n/a	n/a
40	ESR1	chr12:26348220-26348796	ECC-1	luminal epithelium:	n/a	n/a
41	REST	chr12:26348251-26348584	ECC-1	luminal epithelium:	n/a	n/a
42	POLR2A	chr12:26347965-26349671	PANC-1	pancreas:	n/a	n/a
43	TEAD4	chr12:26348113-26349245	ECC-1	luminal epithelium:	n/a	n/a
44	TCF12	chr12:26348019-26348615	ECC-1	luminal epithelium:	n/a	n/a
45	MAX	chr12:26348031-26349393	A549	lung:	n/a	n/a
46	MAX	chr12:26348203-26349295	SK-N-SH	brain:	n/a	n/a
47	POLR2A	chr12:26348252-26349251	H1-hESC	embryonic stem cell:	n/a	n/a
48	YY1	chr12:26348126-26349328	SK-N-SH	brain:	n/a	chr12:26349050-26349061
49	MAX	chr12:26348211-26349208	MCF-7	breast:	n/a	n/a
50	POLR2A	chr12:26348174-26348513	H1-neurons	neurons:	n/a	n/a

No data

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SSPN-3	chr12:26348289-26348464	NONHSAT027395
2	lnc-SSPN-3	chr12:26348160-26348546	l_621_chr12:26342464-26348546_testes

No data

Variant related genes	Relation type
SSPN	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12314653	0.80[ASN][1000 genomes]
rs12315774	0.80[ASN][1000 genomes]
rs12316258	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12582448	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs12810386	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12818201	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs1480036	0.85[ASN][1000 genomes]
rs16930329	0.85[ASN][1000 genomes]
rs17380837	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34004743	0.85[ASN][1000 genomes]
rs34218011	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs34583201	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs35722594	0.80[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs3809138	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61914465	0.80[ASN][1000 genomes]
rs7955859	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7976236	0.80[ASN][1000 genomes]
rs875295	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]

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	nsv648	chr12:26330291-26375186	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs58747679	SSPN	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26347800-26349000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:26347800-26349200	Active TSS	Duodenum Smooth Muscle	Duodenum
3	chr12:26347800-26349600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
4	chr12:26348000-26348400	Flanking Bivalent TSS/Enh	Primary B cells from cord blood	blood
5	chr12:26348000-26348400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr12:26348000-26348400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr12:26348000-26348400	Flanking Active TSS	Liver	Liver
8	chr12:26348000-26348400	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr12:26348000-26348400	Flanking Active TSS	Fetal Muscle Trunk	muscle
10	chr12:26348000-26348400	Flanking Active TSS	A549	lung
11	chr12:26348000-26348400	Flanking Active TSS	NH-A	brain
12	chr12:26348000-26348400	Flanking Active TSS	Osteobl	bone
13	chr12:26348000-26348600	Active TSS	Esophagus	oesophagus
14	chr12:26348000-26348600	Active TSS	Fetal Stomach	stomach
15	chr12:26348000-26348800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
16	chr12:26348000-26348800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr12:26348000-26348800	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
18	chr12:26348000-26348800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr12:26348000-26348800	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
20	chr12:26348000-26348800	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr12:26348000-26348800	Active TSS	Muscle Satellite Cultured Cells	--
22	chr12:26348000-26348800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr12:26348000-26348800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr12:26348000-26348800	Active TSS	Adipose Nuclei	Adipose
25	chr12:26348000-26348800	Active TSS	Duodenum Mucosa	Duodenum
26	chr12:26348000-26348800	Bivalent/Poised TSS	Fetal Adrenal Gland	Adrenal Gland
27	chr12:26348000-26348800	Bivalent/Poised TSS	Fetal Brain Female	brain
28	chr12:26348000-26348800	Active TSS	Pancreas	Pancrea
29	chr12:26348000-26348800	Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr12:26348000-26348800	Bivalent/Poised TSS	GM12878-XiMat	blood
31	chr12:26348000-26348800	Active TSS	HUVEC	blood vessel
32	chr12:26348000-26348800	Active TSS	NHDF-Ad	bronchial
33	chr12:26348000-26349000	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr12:26348000-26349000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
35	chr12:26348000-26349000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr12:26348000-26349000	Active TSS	Brain Angular Gyrus	brain
37	chr12:26348000-26349000	Bivalent/Poised TSS	Fetal Thymus	thymus
38	chr12:26348000-26349000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
39	chr12:26348000-26349200	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
40	chr12:26348000-26349200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr12:26348000-26349200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr12:26348000-26349200	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr12:26348000-26349200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr12:26348000-26349200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:26348000-26349200	Active TSS	Breast Myoepithelial Primary Cells	Breast
46	chr12:26348000-26349200	Active TSS	Brain Hippocampus Middle	brain
47	chr12:26348000-26349200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
48	chr12:26348000-26349200	Active TSS	Fetal Intestine Large	intestine
49	chr12:26348000-26349200	Active TSS	Fetal Intestine Small	intestine
50	chr12:26348000-26349200	Active TSS	Rectal Mucosa Donor 31	rectum

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