Variant report

Variant	rs12040384
Chromosome Location	chr1:151226182-151226183
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:28)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr1:151225804-151226225	SK-N-MC	brain:	n/a	n/a

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:151226139-151226189	HL-60	blood:	n/a
2	chr1:151226139-151226189	NT2-D1	testis:	n/a
3	chr1:151226139-151226189	BE2_C	brain:	n/a
4	chr1:151226139-151226189	SK-N-MC	brain:	n/a
5	chr1:151226139-151226189	SKMC	muscle:	n/a
6	chr1:151226139-151226189	LNCaP	prostate:	n/a
7	chr1:151226139-151226189	NH-A	brain:	n/a
8	chr1:151226139-151226189	HMEC	breast:	n/a
9	chr1:151226139-151226189	HRCEpiC	kidney:	n/a
10	chr1:151226139-151226189	Hepatocyte	liver:	n/a
11	chr1:151226139-151226189	AG04450	lung:	fetal
12	chr1:151226139-151226189	HAEpiC	amniotic membrane:	n/a
13	chr1:151226139-151226189	HRPEpiC	eye:	n/a
14	chr1:151226139-151226189	Hela-S3	cervix:	n/a
15	chr1:151226139-151226189	T-47D	breast:	n/a
16	chr1:151226139-151226189	RPTEC	kidney:	n/a
17	chr1:151226139-151226189	SAEC	small airway:	n/a
18	chr1:151226139-151226189	MCF-7	breast:	n/a
19	chr1:151226139-151226189	HCPEpiC	choroid plexus:	n/a
20	chr1:151226139-151226189	NB4	blood:	n/a
21	chr1:151226139-151226189	HEK293	kidney:	embryo
22	chr1:151226139-151226189	Caco-2	colon:	n/a
23	chr1:151226139-151226189	H1-hESC	embryonic stem cell:	embryo
24	chr1:151226139-151226189	ovcar-3	ovarian:	n/a
25	chr1:151226139-151226189	HCM	heart:	n/a
26	chr1:151226139-151226189	BJ	skin:	n/a
27	chr1:151226139-151226189	HIPEpiC	eye:	n/a
28	chr1:151226139-151226189	PrEC	prostate:	n/a
29	chr1:151226139-151226189	HEEpiC	esophagus:	n/a
30	chr1:151226139-151226189	HNPCEpiC	eye:	n/a
31	chr1:151226139-151226189	CMK	blood:	n/a
32	chr1:151226139-151226189	K562	blood:	n/a
33	chr1:151226139-151226189	GM12878	blood:	n/a
34	chr1:151226139-151226189	HRE	kidney:	n/a
35	chr1:151226139-151226189	AG09319	gingival:	n/a
36	chr1:151226139-151226189	ProgFib	skin:	n/a
37	chr1:151226139-151226189	HUVEC	blood vessel:	n/a
38	chr1:151226139-151226189	HCF	heart:	n/a
39	chr1:151226139-151226189	U87	brain:	n/a
40	chr1:151226139-151226189	HepG2	liver:	n/a
41	chr1:151226139-151226189	GM19239	blood:	n/a
42	chr1:151226139-151226189	SK-N-SH_RA	brain:	n/a
43	chr1:151226139-151226189	ECC-1	luminal epithelium:	n/a
44	chr1:151226139-151226189	PANC-1	pancreas:	n/a
45	chr1:151226139-151226189	Jurkat	blood:	n/a
46	chr1:151226139-151226189	SK-N-SH	brain:	n/a
47	chr1:151226139-151226189	AG10803	skin:	n/a
48	chr1:151226139-151226189	NHDF-neo	bronchial:	n/a
49	chr1:151226139-151226189	AG09309	skin:	n/a
50	chr1:151226139-151226189	NHBE	bronchial:	n/a

(count:28 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:151222463..151229121-chr1:151253476..151256667,10	MCF-7	breast:
2	chr1:151104720..151106721-chr1:151225505..151227550,2	MCF-7	breast:
3	chr1:151225447..151227979-chr1:151803297..151804971,2	K562	blood:
4	1:151219411-151234038..1:151592347-151603110	K562	blood:
5	chr1:151159342..151162316-chr1:151225405..151226979,2	MCF-7	breast:
6	1:151171193-151178589..1:151219411-151234038	GM12878	blood:
7	chr1:151118376..151121066-chr1:151225165..151227350,2	MCF-7	breast:
8	chr1:151225998..151229280-chr1:151252382..151256725,6	K562	blood:
9	chr1:151042160..151045059-chr1:151225748..151228568,3	MCF-7	breast:
10	chr1:151161246..151164199-chr1:151225509..151227562,3	K562	blood:
11	chr1:151042221..151044352-chr1:151224513..151226918,2	K562	blood:
12	chr1:151225526..151228725-chr1:151252382..151257550,9	K562	blood:
13	chr1:151169798..151173171-chr1:151225503..151227858,3	K562	blood:
14	chr1:151226153..151228488-chr1:151257371..151260075,3	MCF-7	breast:
15	chr1:151225781..151228745-chr1:151734591..151737226,2	K562	blood:
16	chr1:151225633..151229215-chr1:151231593..151235514,4	MCF-7	breast:
17	chr1:151170887..151173171-chr1:151225503..151227858,2	K562	blood:
18	chr1:150997028..150998555-chr1:151224004..151226957,2	MCF-7	breast:
19	chr1:151225972..151227496-chr2:65354463..65357441,2	MCF-7	breast:
20	chr1:151030654..151033886-chr1:151224560..151228363,4	MCF-7	breast:
21	chr1:151138869..151140924-chr1:151225967..151227871,3	MCF-7	breast:
22	chr1:151138069..151139851-chr1:151225376..151227012,2	MCF-7	breast:
23	chr1:151169497..151174843-chr1:151224312..151231181,18	MCF-7	breast:
24	chr1:151127203..151129346-chr1:151224584..151227101,2	K562	blood:
25	chr1:151225665..151228952-chr1:151371435..151373604,4	MCF-7	breast:
26	chr1:151224415..151228832-chr1:151251866..151257138,17	MCF-7	breast:
27	chr1:151169931..151174343-chr1:151224824..151227591,5	MCF-7	breast:
28	chr1:151158002..151164153-chr1:151224298..151228623,7	MCF-7	breast:

No data

Variant related genes	Relation type
PSMD4	TF binding region
PSMD4	CpG island
ENSG00000232671	Chromatin interaction
ENSG00000138069	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000143363	Chromatin interaction
ENSG00000163159	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000159377	Chromatin interaction
ENSG00000163155	Chromatin interaction
ENSG00000143373	Chromatin interaction
ENSG00000143398	Chromatin interaction
ENSG00000159352	Chromatin interaction
ENSG00000143434	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000206635	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000163156	Chromatin interaction
ENSG00000163154	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10749660	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10888408	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204791	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11204795	0.83[ASN][1000 genomes]
rs12022732	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12048670	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12062719	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12407426	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16827941	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs16833079	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1892196	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2275900	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs41302131	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4291501	0.82[ASN][1000 genomes]
rs4520422	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4971013	0.83[ASN][1000 genomes]
rs4971015	0.90[ASN][1000 genomes]
rs4971016	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971021	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4971023	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4971025	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971026	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4971027	0.81[ASN][1000 genomes]
rs58323986	0.81[ASN][1000 genomes]
rs61817972	0.88[ASN][1000 genomes]
rs6587559	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6587562	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6681071	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6681163	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6683396	0.83[ASN][1000 genomes]
rs6686402	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6695344	0.88[ASN][1000 genomes]
rs6701325	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7521064	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7527032	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7532935	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7539584	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7544947	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[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

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151173200-151227200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:151195200-151227200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:151206800-151226600	Weak transcription	Right Atrium	heart
4	chr1:151212400-151226800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr1:151213200-151226800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:151216000-151227200	Weak transcription	Fetal Heart	heart
7	chr1:151216400-151226800	Weak transcription	Fetal Brain Male	brain
8	chr1:151216600-151226800	Weak transcription	Brain Angular Gyrus	brain
9	chr1:151219000-151226800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr1:151220600-151226800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
11	chr1:151220800-151226600	Weak transcription	Psoas Muscle	Psoas
12	chr1:151220800-151226600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr1:151220800-151226800	Weak transcription	Small Intestine	intestine
14	chr1:151221000-151226800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr1:151221200-151226600	Weak transcription	Primary hematopoietic stem cells	blood
16	chr1:151221200-151226600	Weak transcription	Colonic Mucosa	Colon
17	chr1:151221200-151226800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
18	chr1:151221200-151226800	Weak transcription	Fetal Kidney	kidney
19	chr1:151221400-151226800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:151221600-151226800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr1:151221600-151226800	Weak transcription	Gastric	stomach
22	chr1:151221600-151226800	Weak transcription	HUVEC	blood vessel
23	chr1:151221800-151226600	Weak transcription	Brain Germinal Matrix	brain
24	chr1:151221800-151226600	Weak transcription	Right Ventricle	heart
25	chr1:151221800-151226600	Weak transcription	Hela-S3	cervix
26	chr1:151221800-151226800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:151221800-151226800	Weak transcription	Pancreas	Pancrea
28	chr1:151222200-151226800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr1:151222200-151226800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr1:151222200-151226800	Weak transcription	Lung	lung
31	chr1:151222200-151226800	Weak transcription	Rectal Mucosa Donor 31	rectum
32	chr1:151222400-151226400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr1:151222400-151226400	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr1:151222400-151226600	Weak transcription	Primary B cells from peripheral blood	blood
35	chr1:151222400-151226600	Weak transcription	Primary T cells fromperipheralblood	blood
36	chr1:151222400-151226600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr1:151222400-151226600	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:151222400-151226600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr1:151222400-151226600	Weak transcription	Brain Anterior Caudate	brain
40	chr1:151222400-151226600	Weak transcription	Fetal Brain Female	brain
41	chr1:151222400-151226600	Weak transcription	Fetal Intestine Large	intestine
42	chr1:151222400-151226600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr1:151222400-151226800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr1:151222400-151226800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr1:151222400-151226800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:151222400-151226800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr1:151222400-151226800	Weak transcription	Aorta	Aorta
48	chr1:151222400-151226800	Weak transcription	Duodenum Mucosa	Duodenum
49	chr1:151222400-151226800	Weak transcription	Esophagus	oesophagus
50	chr1:151222400-151226800	Weak transcription	Skeletal Muscle Male	skeletal muscle

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