Variant report

Variant	rs45560933
Chromosome Location	chr2:113930840-113930841
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:122)
Chromatin interactive
region (count:3)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr2:113930729-113931042	K562	blood:	n/a	n/a
2	POLR2A	chr2:113930698-113934407	GM12878	blood:	n/a	n/a
3	RCOR1	chr2:113930812-113931721	K562	blood:	n/a	n/a
4	POLR2A	chr2:113930686-113935532	GM12891	blood:	n/a	n/a
5	PML	chr2:113930798-113933468	GM12878	blood:	n/a	chr2:113933381-113933389
6	CBX3	chr2:113930739-113931768	K562	blood:	n/a	n/a
7	CHD2	chr2:113930802-113931737	GM12878	blood:	n/a	n/a
8	MTA3	chr2:113930698-113933933	GM12878	blood:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:113930819-113930869	HCF	heart:	n/a
2	chr2:113930840-113930890	PFSK-1	brain:	n/a
3	chr2:113930840-113930890	BE2_C	brain:	n/a
4	chr2:113930840-113930890	HL-60	blood:	n/a
5	chr2:113930840-113930890	AG10803	skin:	n/a
6	chr2:113930819-113930869	HRPEpiC	eye:	n/a
7	chr2:113930840-113930890	GM12891	blood:	n/a
8	chr2:113930840-113930890	GM12878	blood:	n/a
9	chr2:113930840-113930890	AG09319	gingival:	n/a
10	chr2:113930819-113930869	AG04449	skin:	fetal
11	chr2:113930840-113930890	ProgFib	skin:	n/a
12	chr2:113930840-113930890	AG04449	skin:	fetal
13	chr2:113930819-113930869	HCPEpiC	choroid plexus:	n/a
14	chr2:113930840-113930890	SAEC	small airway:	n/a
15	chr2:113930819-113930869	NHDF-neo	bronchial:	n/a
16	chr2:113930840-113930890	HEK293	kidney:	embryo
17	chr2:113930819-113930869	LNCaP	prostate:	n/a
18	chr2:113930819-113930869	AoSMC	blood vessel:	n/a
19	chr2:113930819-113930869	SK-N-SH	brain:	n/a
20	chr2:113930819-113930869	CMK	blood:	n/a
21	chr2:113930819-113930869	HMEC	breast:	n/a
22	chr2:113930840-113930890	A549	lung:	n/a
23	chr2:113930840-113930890	K562	blood:	n/a
24	chr2:113930840-113930890	BJ	skin:	n/a
25	chr2:113930819-113930869	AG10803	skin:	n/a
26	chr2:113930840-113930890	Caco-2	colon:	n/a
27	chr2:113930819-113930869	T-47D	breast:	n/a
28	chr2:113930819-113930869	GM06990	blood:	n/a
29	chr2:113930840-113930890	RPTEC	kidney:	n/a
30	chr2:113930819-113930869	HRE	kidney:	n/a
31	chr2:113930840-113930890	CMK	blood:	n/a
32	chr2:113930819-113930869	NHBE	bronchial:	n/a
33	chr2:113930819-113930869	HCT-116	colon:	n/a
34	chr2:113930840-113930890	PANC-1	pancreas:	n/a
35	chr2:113930819-113930869	HAEpiC	amniotic membrane:	n/a
36	chr2:113930819-113930869	IMR90	lung:	fetal
37	chr2:113930840-113930890	PrEC	prostate:	n/a
38	chr2:113930819-113930869	SK-N-SH_RA	brain:	n/a
39	chr2:113930840-113930890	NB4	blood:	n/a
40	chr2:113930819-113930869	SK-N-MC	brain:	n/a
41	chr2:113930819-113930869	HL-60	blood:	n/a
42	chr2:113930819-113930869	A549	lung:	n/a
43	chr2:113930819-113930869	PFSK-1	brain:	n/a
44	chr2:113930840-113930890	GM06990	blood:	n/a
45	chr2:113930840-113930890	HRCEpiC	kidney:	n/a
46	chr2:113930840-113930890	HCF	heart:	n/a
47	chr2:113930840-113930890	HUVEC	blood vessel:	n/a
48	chr2:113930819-113930869	SKMC	muscle:	n/a
49	chr2:113930819-113930869	BJ	skin:	n/a
50	chr2:113930819-113930869	MCF-7	breast:	n/a

(count:3 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113930203..113932925-chr2:113950004..113952772,2	K562	blood:
2	chr2:113919676..113922508-chr2:113929408..113931402,2	K562	blood:
3	chr2:113913826..113916797-chr2:113930139..113933348,3	K562	blood:

No data

Variant related genes	Relation type
PSD4	TF binding region
PSD4	CpG island
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12711763	0.96[ASN][1000 genomes]
rs13382259	0.96[ASN][1000 genomes]
rs13400502	0.96[ASN][1000 genomes]
rs13419549	0.96[ASN][1000 genomes]
rs3738908	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs45550936	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45603540	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6542123	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113916000-113939000	Weak transcription	Right Atrium	heart
2	chr2:113923000-113931200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:113923000-113932200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:113923000-113956000	Weak transcription	HMEC	breast
6	chr2:113923200-113931600	Weak transcription	Brain Anterior Caudate	brain
7	chr2:113923800-113931400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:113923800-113937800	Weak transcription	H1 Cell Line	embryonic stem cell
9	chr2:113925400-113931000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr2:113926600-113931000	Enhancers	Primary T cells fromperipheralblood	blood
11	chr2:113926600-113931000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr2:113926600-113932600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr2:113926800-113931000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:113926800-113931000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr2:113926800-113931200	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:113926800-113931600	Weak transcription	Esophagus	oesophagus
17	chr2:113927600-113936200	Weak transcription	NHEK	skin
18	chr2:113928000-113935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:113928400-113931200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr2:113928600-113931000	Enhancers	HepG2	liver
21	chr2:113928600-113931200	Enhancers	Fetal Thymus	thymus
22	chr2:113928600-113931600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr2:113929600-113932800	Enhancers	Stomach Mucosa	stomach
24	chr2:113930000-113931000	Enhancers	Primary hematopoietic stem cells	blood
25	chr2:113930000-113931000	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr2:113930000-113931000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr2:113930000-113931200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr2:113930000-113931400	Flanking Active TSS	Primary T cells from cord blood	blood
29	chr2:113930200-113931000	Enhancers	Duodenum Mucosa	Duodenum
30	chr2:113930200-113931000	Enhancers	Spleen	Spleen
31	chr2:113930200-113931200	Enhancers	Thymus	Thymus
32	chr2:113930200-113931400	Enhancers	Liver	Liver
33	chr2:113930200-113931600	Enhancers	Colonic Mucosa	Colon
34	chr2:113930200-113931600	Enhancers	Placenta	Placenta
35	chr2:113930200-113931600	Enhancers	Gastric	stomach
36	chr2:113930200-113931600	Enhancers	Lung	lung
37	chr2:113930200-113935200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr2:113930400-113931000	Enhancers	K562	blood
39	chr2:113930400-113931400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
40	chr2:113930400-113934200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
41	chr2:113930600-113931000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr2:113930600-113931400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr2:113930600-113931400	Flanking Active TSS	Dnd41	blood
44	chr2:113930600-113931600	Weak transcription	Fetal Intestine Small	intestine
45	chr2:113930600-113931600	Weak transcription	Small Intestine	intestine
46	chr2:113930600-113934200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr2:113930600-113934600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr2:113930800-113931200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
49	chr2:113930800-113931200	Weak transcription	Fetal Intestine Large	intestine
50	chr2:113930800-113931200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum

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