Variant report

Variant	rs11584388
Chromosome Location	chr1:151169752-151169753
allele	G/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:11)
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	POLR2A	chr1:151169542-151169977	HepG2	liver:	n/a	n/a
2	HEY1	chr1:151169464-151170176	HepG2	liver:	n/a	n/a
3	TBP	chr1:151169653-151169889	HepG2	liver:	n/a	n/a
4	POLR2A	chr1:151169633-151169879	HepG2	liver:	n/a	n/a
5	POLR2A	chr1:151169601-151171798	HepG2	liver:	n/a	n/a
6	HA-E2F1	chr1:151169528-151171929	MCF-7	breast:	n/a	chr1:151171348-151171360 chr1:151170424-151170436 chr1:151171010-151171019 chr1:151171669-151171684 chr1:151171348-151171357
7	NR2F2	chr1:151169454-151171865	MCF-7	breast:	n/a	n/a
8	HEY1	chr1:151169585-151169774	HepG2	liver:	n/a	n/a
9	POLR2A	chr1:151168931-151172403	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151169497..151174843-chr1:151224312..151231181,18	MCF-7	breast:
2	chr1:151162057..151164706-chr1:151165181..151172008,8	K562	blood:
3	chr1:151167814..151170369-chr1:151245194..151246986,2	MCF-7	breast:
4	chr1:151166432..151169145-chr1:151169439..151172527,5	MCF-7	breast:
5	chr1:151165541..151174157-chr1:151252015..151257857,16	MCF-7	breast:
6	chr1:151156826..151164982-chr1:151165389..151172985,25	MCF-7	breast:
7	chr1:151136716..151140911-chr1:151168778..151172657,5	MCF-7	breast:
8	chr1:151168724..151174586-chr1:151252405..151256834,10	MCF-7	breast:
9	chr1:151136857..151140256-chr1:151168802..151172321,4	MCF-7	breast:
10	chr1:151041779..151043840-chr1:151166772..151169795,3	MCF-7	breast:
11	chr1:150229637..150231508-chr1:151169443..151171733,2	MCF-7	breast:

No data

Variant related genes	Relation type
VPS72	TF binding region
PIP5K1A	TF binding region
ENSG00000143458	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000271845	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000232671	Chromatin interaction
ENSG00000118298	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11577302	0.89[ASN][1000 genomes]
rs12739135	0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs12743210	0.86[AFR][1000 genomes]
rs16833107	0.82[ASN][1000 genomes]
rs16865250	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35118469	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36035148	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72994055	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1001897	chr1:150743271-151241600	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv535158	chr1:150743271-151241600	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
3	nsv522840	chr1:150933723-151347746	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
4	nsv916272	chr1:150961809-151557253	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	219 gene(s)	inside rSNPs	diseases
5	nsv831559	chr1:151109459-151239921	Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
6	nsv831570	chr1:151129020-151281778	Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	106 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11584388	PSMD4	cis	brain	BrainEAC

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151162800-151170200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
2	chr1:151162800-151170400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:151163000-151170400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:151163200-151170400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:151163200-151170400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr1:151163200-151170400	Weak transcription	Gastric	stomach
7	chr1:151163200-151170400	Weak transcription	Left Ventricle	heart
8	chr1:151163400-151170000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr1:151163400-151170200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr1:151163400-151170200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr1:151163400-151170200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr1:151163400-151170200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr1:151163400-151170200	Weak transcription	Brain Substantia Nigra	brain
14	chr1:151163400-151170400	Weak transcription	Primary T cells from cord blood	blood
15	chr1:151163600-151170200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr1:151163600-151170200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr1:151163600-151170200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr1:151166800-151170200	Active TSS	Rectal Mucosa Donor 29	rectum
19	chr1:151167000-151172000	Active TSS	Colonic Mucosa	Colon
20	chr1:151167200-151169800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr1:151167800-151170200	Enhancers	Fetal Intestine Small	intestine
22	chr1:151168000-151170200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:151168000-151170200	Active TSS	HepG2	liver
24	chr1:151168000-151170400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:151168000-151170400	Weak transcription	Pancreas	Pancrea
26	chr1:151168000-151170800	Weak transcription	Lung	lung
27	chr1:151168200-151170200	Weak transcription	HSMMtube	muscle
28	chr1:151168200-151170200	Weak transcription	NHLF	lung
29	chr1:151168200-151170400	Weak transcription	Fetal Muscle Trunk	muscle
30	chr1:151168600-151170600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr1:151168800-151170200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:151168800-151170200	Weak transcription	Brain Hippocampus Middle	brain
33	chr1:151168800-151170200	Weak transcription	Fetal Muscle Leg	muscle
34	chr1:151169000-151170000	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr1:151169000-151170000	Weak transcription	NHEK	skin
36	chr1:151169000-151170200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr1:151169000-151170200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr1:151169000-151170200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr1:151169000-151170200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr1:151169000-151170200	Weak transcription	GM12878-XiMat	blood
41	chr1:151169000-151170200	Weak transcription	HSMM	muscle
42	chr1:151169000-151170200	Weak transcription	HUVEC	blood vessel
43	chr1:151169000-151170200	Weak transcription	K562	blood
44	chr1:151169000-151170200	Weak transcription	NH-A	brain
45	chr1:151169000-151170200	Weak transcription	NHDF-Ad	bronchial
46	chr1:151169200-151170000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:151169200-151170000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
48	chr1:151169200-151170000	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:151169200-151170000	Weak transcription	A549	lung
50	chr1:151169200-151170200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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