Variant report

Variant	rs9895764
Chromosome Location	chr17:45927961-45927962
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 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	chr17:45912259..45914443-chr17:45925886..45928377,3	MCF-7	breast:
5	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
6	chr17:45927380..45931249-chr17:45931939..45938449,12	K562	blood:
7	chr17:45927036..45931880-chr17:45931939..45936922,11	K562	blood:
8	chr17:45912279..45914440-chr17:45926481..45928555,2	K562	blood:
9	chr17:45925187..45928793-chr17:46033650..46037470,3	MCF-7	breast:
10	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000108439	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000167182	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000075624	Chromatin interaction
ENSG00000167183	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11079797	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs16948424	0.86[EUR][1000 genomes]
rs16948662	0.98[EUR][1000 genomes]
rs2010952	0.86[EUR][1000 genomes]
rs34156395	0.88[EUR][1000 genomes]
rs59111282	0.88[EUR][1000 genomes]
rs62076106	0.86[EUR][1000 genomes]
rs6503875	0.98[EUR][1000 genomes]
rs7212099	1.00[EUR][1000 genomes]
rs7214694	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8078688	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs916798	0.86[EUR][1000 genomes]
rs9896712	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9897598	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9903904	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9904503	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9915028	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9895764	SCRN2	cis	lung	GTEx
rs9895764	SCRN2	cis	Skin Sun Exposed Lower leg	GTEx
rs9895764	SCRN2	cis	Esophagus Muscularis	GTEx
rs9895764	SCRN2	cis	Muscle Skeletal	GTEx
rs9895764	SCRN2	cis	Stomach	GTEx
rs9895764	SCRN2	cis	Whole Blood	GTEx
rs9895764	SCRN2	Cis_1M	lymphoblastoid	RTeQTL
rs9895764	SCRN2	cis	Adipose Subcutaneous	GTEx
rs9895764	SCRN2	cis	Esophagus Mucosa	GTEx

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45919200-45928000	Weak transcription	Right Atrium	heart
2	chr17:45924200-45928000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
3	chr17:45925800-45928000	Weak transcription	Lung	lung
4	chr17:45926400-45929000	Flanking Active TSS	Placenta	Placenta
5	chr17:45926600-45930000	Bivalent Enhancer	Fetal Thymus	thymus
6	chr17:45926800-45928200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr17:45926800-45928200	Flanking Active TSS	Placenta Amnion	Placenta Amnion
8	chr17:45927000-45928000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr17:45927200-45928000	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
10	chr17:45927200-45928200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
11	chr17:45927200-45928200	Bivalent Enhancer	Primary T regulatory cells fromperipheralblood	blood
12	chr17:45927200-45928200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr17:45927200-45928200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr17:45927200-45928200	Flanking Active TSS	NHEK	skin
15	chr17:45927200-45928400	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr17:45927200-45928400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
17	chr17:45927200-45929600	Enhancers	Spleen	Spleen
18	chr17:45927400-45928000	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
19	chr17:45927400-45928000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr17:45927400-45928000	Bivalent Enhancer	Stomach Mucosa	stomach
21	chr17:45927400-45928400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
22	chr17:45927400-45928800	Active TSS	Esophagus	oesophagus
23	chr17:45927400-45929000	Bivalent/Poised TSS	Rectal Smooth Muscle	rectum
24	chr17:45927400-45929800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
25	chr17:45927600-45928000	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell
26	chr17:45927600-45928000	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
27	chr17:45927600-45928000	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
28	chr17:45927600-45928000	Bivalent Enhancer	Primary T helper naive cells fromperipheralblood	blood
29	chr17:45927600-45928000	Bivalent Enhancer	Primary T killer memory cells from peripheral blood	blood
30	chr17:45927600-45928000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
31	chr17:45927600-45928000	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr17:45927600-45928000	Flanking Active TSS	Colonic Mucosa	Colon
33	chr17:45927600-45928000	Enhancers	Pancreas	Pancrea
34	chr17:45927600-45928200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr17:45927600-45928200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
36	chr17:45927600-45928200	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
37	chr17:45927600-45928200	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
38	chr17:45927600-45928200	Flanking Active TSS	A549	lung
39	chr17:45927600-45928200	Flanking Active TSS	K562	blood
40	chr17:45927600-45929600	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
41	chr17:45927600-45929800	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
42	chr17:45927600-45930000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
43	chr17:45927600-45930200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr17:45927600-45930200	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 2	blood
45	chr17:45927800-45928000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr17:45927800-45928000	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr17:45927800-45928000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
48	chr17:45927800-45928000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
49	chr17:45927800-45928000	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
50	chr17:45927800-45928000	Bivalent Enhancer	Adipose Nuclei	Adipose

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