Variant report

Variant	rs2325749
Chromosome Location	chr17:46024973-46024974
allele	G/T
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:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:45995492..45998307-chr17:46023078..46025129,2	MCF-7	breast:
2	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
3	chr17:46023026..46029175-chr17:46044937..46051234,10	K562	blood:
4	chr17:46024307..46025138-chr17:46048069..46048589,2	MCF-7	breast:
5	chr17:46008254..46011151-chr17:46023044..46026189,3	MCF-7	breast:
6	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
7	chr17:46024543..46026331-chr17:46053891..46056374,2	K562	blood:
8	chr17:46024094..46025050-chr17:46033196..46033701,2	K562	blood:
9	chr17:45976149..45977762-chr17:46023014..46025634,2	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PRR15L-2	chr17:46024921-46025008	ENSG00000264019.1

No data

Variant related genes	Relation type
ENSG00000167182	Chromatin interaction
ENSG00000266601	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000108465	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11079803	0.81[ASN][1000 genomes]
rs1108833	0.82[AMR][1000 genomes]
rs11652185	0.81[ASN][1000 genomes]
rs11654010	0.81[AMR][1000 genomes]
rs11870852	0.85[AMR][1000 genomes]
rs12601827	0.81[ASN][1000 genomes]
rs12602494	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17616603	0.81[AMR][1000 genomes]
rs2325751	0.81[ASN][1000 genomes]
rs2525107	0.89[EUR][1000 genomes]
rs3096	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35280206	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35336840	0.81[AMR][1000 genomes]
rs3764396	0.81[ASN][1000 genomes]
rs4793731	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4793732	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4793733	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4793737	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4794261	0.85[AMR][1000 genomes]
rs4794286	0.85[AMR][1000 genomes]
rs4794332	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7211859	0.85[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
4	esv1000014	chr17:46019228-46029457	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2325749	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46019600-46027000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr17:46019800-46025600	Weak transcription	HSMM	muscle
3	chr17:46019800-46026800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr17:46019800-46026800	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr17:46019800-46026800	Weak transcription	Brain Germinal Matrix	brain
6	chr17:46019800-46026800	Weak transcription	HSMMtube	muscle
7	chr17:46019800-46027400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr17:46019800-46034200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr17:46019800-46047600	Weak transcription	Aorta	Aorta
10	chr17:46020000-46026000	Weak transcription	Fetal Heart	heart
11	chr17:46020000-46026200	Weak transcription	Fetal Kidney	kidney
12	chr17:46020000-46026400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr17:46020000-46026400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
14	chr17:46020000-46026400	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr17:46020000-46026800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr17:46020000-46026800	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr17:46020000-46027000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr17:46020000-46034600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr17:46020200-46026000	Weak transcription	NHDF-Ad	bronchial
20	chr17:46020200-46026200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr17:46020200-46026200	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr17:46020200-46026800	Weak transcription	HUVEC	blood vessel
23	chr17:46020800-46025800	Genic enhancers	HepG2	liver
24	chr17:46021600-46026200	Strong transcription	Sigmoid Colon	Sigmoid Colon
25	chr17:46022800-46026200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr17:46022800-46026400	Weak transcription	Primary hematopoietic stem cells	blood
27	chr17:46023000-46026200	Weak transcription	NH-A	brain
28	chr17:46023000-46026400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr17:46023000-46026600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr17:46023000-46026800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr17:46023200-46026600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr17:46023200-46026600	Weak transcription	Fetal Brain Female	brain
33	chr17:46023200-46026800	Genic enhancers	Fetal Intestine Small	intestine
34	chr17:46023200-46030000	Genic enhancers	Fetal Intestine Large	intestine
35	chr17:46023400-46025800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr17:46023400-46026000	Strong transcription	Brain Anterior Caudate	brain
37	chr17:46023600-46026000	Weak transcription	Primary B cells from cord blood	blood
38	chr17:46023600-46026000	Weak transcription	Esophagus	oesophagus
39	chr17:46023600-46026000	Weak transcription	Gastric	stomach
40	chr17:46023600-46026000	Enhancers	Rectal Mucosa Donor 31	rectum
41	chr17:46023600-46026200	Weak transcription	Left Ventricle	heart
42	chr17:46023600-46026800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr17:46023800-46026200	Weak transcription	Rectal Smooth Muscle	rectum
44	chr17:46024000-46025400	Weak transcription	Duodenum Mucosa	Duodenum
45	chr17:46024000-46025400	Weak transcription	HMEC	breast
46	chr17:46024000-46025600	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr17:46024000-46026000	Weak transcription	Adipose Nuclei	Adipose
48	chr17:46024000-46026200	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr17:46024000-46026200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr17:46024000-46026400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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