Variant report

Variant	rs9903904
Chromosome Location	chr17:45929169-45929170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:9)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:9 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SIN3AK20	chr17:45929079-45929623	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr17:45928258-45929428	K562	blood:	n/a	n/a
3	ZBTB7A	chr17:45928243-45929366	K562	blood:	n/a	n/a
4	POLR2A	chr17:45929125-45930569	H1-neurons	neurons:	n/a	n/a
5	ELF1	chr17:45928735-45929322	K562	blood:	n/a	n/a
6	ELF1	chr17:45929112-45929484	GM12878	blood:	n/a	n/a
7	MAZ	chr17:45927924-45929878	K562	blood:	n/a	chr17:45928574-45928584 chr17:45928699-45928709
8	POLR2A	chr17:45927534-45930018	K562	blood:	n/a	n/a
9	SIN3A	chr17:45927995-45929499	H1-hESC	embryonic stem cell:	n/a	chr17:45929278-45929286

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr17:45927242..45929769-chr17:46017796..46019388,2	MCF-7	breast:
2	chr17:45926861..45929500-chr7:5568593..5570213,2	MCF-7	breast:
3	chr17:45924111..45929589-chr17:45940263..45947435,9	MCF-7	breast:
4	chr17:45918541..45919517-chr17:45928758..45929512,2	K562	blood:
5	chr17:45928961..45933138-chr17:45960892..45963467,3	K562	blood:
6	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
7	chr17:45928850..45930934-chr17:46029439..46031345,2	K562	blood:
8	chr17:45927380..45931249-chr17:45931939..45938449,12	K562	blood:
9	chr17:45925951..45927687-chr17:45928711..45930678,2	K562	blood:
10	chr17:45927036..45931880-chr17:45931939..45936922,11	K562	blood:
11	chr17:45928921..45932195-chr17:46017729..46021262,3	MCF-7	breast:
12	chr17:45907387..45909991-chr17:45928355..45930503,2	MCF-7	breast:
13	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:
14	chr17:45928046..45933138-chr17:45958246..45966286,8	K562	blood:

No data

Variant related genes	Relation type
SP6	TF binding region
ENSG00000075624	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000167182	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11079797	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11079798	0.85[EUR][1000 genomes]
rs11651698	0.87[EUR][1000 genomes]
rs2074185	0.89[EUR][1000 genomes]
rs4794202	0.88[EUR][1000 genomes]
rs4794204	0.85[EUR][1000 genomes]
rs59715174	0.89[EUR][1000 genomes]
rs62066132	0.85[EUR][1000 genomes]
rs7214694	0.93[ASN][1000 genomes]
rs8078688	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9895764	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9896712	0.89[ASN][1000 genomes]
rs9897598	0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9904503	0.86[ASN][1000 genomes]
rs9915028	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9903904	SCRN2	cis	Esophagus Mucosa	GTEx
rs9903904	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs9903904	SCRN2	cis	lung	GTEx
rs9903904	SCRN2	cis	Stomach	GTEx
rs9903904	SLC17A3	trans	lymphoblastoid	RTeQTL
rs9903904	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs9903904	SCRN2	cis	Adipose Subcutaneous	GTEx
rs9903904	SCRN2	cis	Esophagus Muscularis	GTEx
rs9903904	SCRN2	cis	Muscle Skeletal	GTEx
rs9903904	SCRN2	cis	Whole Blood	GTEx

Chromatin state (count:82 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45926600-45930000	Bivalent Enhancer	Fetal Thymus	thymus
2	chr17:45927200-45929600	Enhancers	Spleen	Spleen
3	chr17:45927400-45929800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr17:45927600-45929600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
5	chr17:45927600-45929800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
6	chr17:45927600-45930000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
7	chr17:45927600-45930200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
8	chr17:45927600-45930200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
9	chr17:45927800-45930000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr17:45928000-45929600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
11	chr17:45928000-45929800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr17:45928200-45929200	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
13	chr17:45928200-45929200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr17:45928200-45929200	Active TSS	K562	blood
15	chr17:45928200-45929200	Active TSS	NHEK	skin
16	chr17:45928200-45929400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr17:45928200-45929400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
18	chr17:45928200-45929400	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
19	chr17:45928200-45929400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
20	chr17:45928200-45929400	Bivalent Enhancer	Small Intestine	intestine
21	chr17:45928200-45929600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr17:45928200-45930000	Bivalent Enhancer	Primary hematopoietic stem cells	blood
23	chr17:45928200-45930000	Bivalent Enhancer	Stomach Mucosa	stomach
24	chr17:45928200-45930200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
25	chr17:45928400-45929200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr17:45928400-45929200	Enhancers	Primary B cells from cord blood	blood
27	chr17:45928400-45929200	Bivalent Enhancer	Brain Inferior Temporal Lobe	brain
28	chr17:45928400-45929600	Bivalent/Poised TSS	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr17:45928400-45929600	Bivalent Enhancer	NH-A	brain
30	chr17:45928400-45930200	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle
31	chr17:45928400-45931400	Bivalent Enhancer	Fetal Muscle Leg	muscle
32	chr17:45928400-45931400	Enhancers	Lung	lung
33	chr17:45928600-45929200	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr17:45928600-45929200	Weak transcription	Gastric	stomach
35	chr17:45928600-45929400	Bivalent Enhancer	HSMM	muscle
36	chr17:45928600-45929600	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
37	chr17:45928600-45929600	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
38	chr17:45928600-45929800	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:45928600-45929800	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr17:45928600-45929800	Bivalent Enhancer	Primary T helper naive cells from peripheral blood	blood
41	chr17:45928600-45929800	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
42	chr17:45928600-45929800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
43	chr17:45928600-45929800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr17:45928600-45929800	Enhancers	Placenta Amnion	Placenta Amnion
45	chr17:45928600-45929800	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
46	chr17:45928800-45929800	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
47	chr17:45928800-45929800	Bivalent Enhancer	Fetal Muscle Trunk	muscle
48	chr17:45928800-45929800	Bivalent Enhancer	Left Ventricle	heart
49	chr17:45928800-45930000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
50	chr17:45928800-45930000	Bivalent Enhancer	Fetal Lung	lung

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