Variant report

Variant	rs3811414
Chromosome Location	chr1:151763246-151763247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	UBTF	chr1:151762667-151763446	K562	blood:	n/a	n/a
2	HDAC2	chr1:151762485-151763768	MCF-7	breast:	n/a	n/a
3	SIN3AK20	chr1:151763037-151763520	SK-N-SH	brain:	n/a	n/a
4	JUND	chr1:151762648-151763398	K562	blood:	n/a	chr1:151763172-151763181
5	EP300	chr1:151762809-151763411	SK-N-SH_RA	brain:	n/a	n/a
6	MAZ	chr1:151762656-151763579	GM12878	blood:	n/a	n/a
7	CREB1	chr1:151762604-151763745	HepG2	liver:	n/a	n/a
8	FOS	chr1:151762879-151763423	GM12878	blood:	n/a	chr1:151763172-151763181
9	TBP	chr1:151762804-151763412	GM12878	blood:	n/a	n/a
10	GTF2F1	chr1:151762993-151763493	Hela-S3	cervix:	n/a	n/a
11	SP1	chr1:151762675-151763503	H1-hESC	embryonic stem cell:	n/a	chr1:151763004-151763013 chr1:151763169-151763190 chr1:151763004-151763013 chr1:151763003-151763015 chr1:151763005-151763014
12	HDAC2	chr1:151762308-151764216	MCF-7	breast:	n/a	n/a
13	POLR2A	chr1:151762743-151763523	GM18505	blood:	n/a	n/a
14	SP2	chr1:151762771-151763471	K562	blood:	n/a	chr1:151763171-151763181
15	SIN3AK20	chr1:151763191-151763759	H1-hESC	embryonic stem cell:	n/a	n/a
16	NFYA	chr1:151762604-151763497	GM12878	blood:	n/a	chr1:151763168-151763183 chr1:151763168-151763183 chr1:151763168-151763182 chr1:151763170-151763180
17	SP1	chr1:151762792-151763591	GM12878	blood:	n/a	chr1:151763004-151763013 chr1:151763169-151763190 chr1:151763004-151763013 chr1:151763003-151763015 chr1:151763005-151763014
18	GATA3	chr1:151762729-151763609	T-47D	breast:	n/a	n/a
19	ELF1	chr1:151762769-151763433	A549	lung:	n/a	n/a
20	ZMIZ1	chr1:151762842-151763412	K562	blood:	n/a	n/a
21	PML	chr1:151762413-151763851	MCF-7	breast:	n/a	n/a
22	SIN3AK20	chr1:151762260-151764320	MCF-7	breast:	n/a	n/a
23	TCF12	chr1:151762601-151763691	ECC-1	luminal epithelium:	n/a	chr1:151763212-151763219
24	MAX	chr1:151762519-151763690	A549	lung:	n/a	n/a
25	FOS	chr1:151762860-151763458	K562	blood:	n/a	chr1:151763172-151763181
26	POLR2A	chr1:151762737-151763460	HCT-116	colon:	n/a	n/a
27	ELF1	chr1:151762740-151763391	K562	blood:	n/a	n/a
28	RCOR1	chr1:151762583-151764112	K562	blood:	n/a	n/a
29	TCF12	chr1:151762529-151763726	A549	lung:	n/a	chr1:151763212-151763219
30	TAL1	chr1:151763172-151763443	K562	blood:	n/a	n/a
31	FOS	chr1:151762999-151763378	MCF10A-Er-Src	breast:	n/a	chr1:151763172-151763181
32	POLR2A	chr1:151763164-151763545	K562	blood:	n/a	n/a
33	MAX	chr1:151762329-151763658	HCT-116	colon:	n/a	n/a
34	WRNIP1	chr1:151763150-151763515	GM12878	blood:	n/a	n/a
35	HCFC1	chr1:151762728-151763558	K562	blood:	n/a	n/a
36	TCF12	chr1:151763072-151763314	GM12878	blood:	n/a	chr1:151763212-151763219
37	CTCF	chr1:151762711-151763269	GM12878	blood:	n/a	chr1:151762795-151762816 chr1:151762800-151762818
38	SIN3AK20	chr1:151763145-151763495	A549	lung:	n/a	n/a
39	CHD2	chr1:151762704-151763559	GM12878	blood:	n/a	n/a
40	EGR1	chr1:151762486-151763462	HCT-116	colon:	n/a	chr1:151763006-151763016 chr1:151763006-151763019 chr1:151763007-151763017 chr1:151762603-151762616 chr1:151763006-151763019 chr1:151763005-151763020 chr1:151762946-151762960 chr1:151763007-151763017 chr1:151763006-151763019 chr1:151763006-151763019 chr1:151763007-151763016 chr1:151763007-151763018 chr1:151763005-151763019
41	HEY1	chr1:151762668-151763571	HepG2	liver:	n/a	n/a
42	FOXM1	chr1:151762557-151763485	GM12878	blood:	n/a	n/a
43	ATF3	chr1:151763010-151763462	A549	lung:	n/a	n/a
44	TEAD4	chr1:151762611-151763634	K562	blood:	n/a	n/a
45	POU2F2	chr1:151762716-151763570	GM12878	blood:	n/a	chr1:151763007-151763019
46	MYC	chr1:151762562-151763667	K562	blood:	n/a	n/a
47	HEY1	chr1:151763209-151763463	HepG2	liver:	n/a	n/a
48	SP2	chr1:151762741-151763521	HepG2	liver:	n/a	chr1:151763171-151763181
49	MAX	chr1:151762638-151763715	SK-N-SH	brain:	n/a	n/a
50	TAF1	chr1:151762605-151763640	ECC-1	luminal epithelium:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:151763213-151763263	AG09319	gingival:	n/a
2	chr1:151763213-151763263	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:151763213-151763263	HRE	kidney:	n/a
4	chr1:151763213-151763263	CMK	blood:	n/a
5	chr1:151763213-151763263	SK-N-SH_RA	brain:	n/a
6	chr1:151763213-151763263	HMEC	breast:	n/a
7	chr1:151763213-151763263	BE2_C	brain:	n/a
8	chr1:151763213-151763263	RPTEC	kidney:	n/a
9	chr1:151763213-151763263	NT2-D1	testis:	n/a
10	chr1:151763213-151763263	Hela-S3	cervix:	n/a
11	chr1:151763213-151763263	GM12891	blood:	n/a
12	chr1:151763213-151763263	A549	lung:	n/a
13	chr1:151763213-151763263	MCF-7	breast:	n/a
14	chr1:151763213-151763263	IMR90	lung:	fetal
15	chr1:151763213-151763263	GM06990	blood:	n/a
16	chr1:151763213-151763263	SK-N-SH	brain:	n/a
17	chr1:151763213-151763263	GM19239	blood:	n/a
18	chr1:151763213-151763263	SAEC	small airway:	n/a
19	chr1:151763213-151763263	AG09309	skin:	n/a
20	chr1:151763213-151763263	K562	blood:	n/a
21	chr1:151763213-151763263	HIPEpiC	eye:	n/a
22	chr1:151763213-151763263	HepG2	liver:	n/a
23	chr1:151763213-151763263	HCT-116	colon:	n/a
24	chr1:151763213-151763263	HEK293	kidney:	embryo
25	chr1:151763213-151763263	NB4	blood:	n/a
26	chr1:151763213-151763263	HAEpiC	amniotic membrane:	n/a
27	chr1:151763213-151763263	HCM	heart:	n/a
28	chr1:151763213-151763263	MCF10A-Er-Src	breast:	n/a
29	chr1:151763213-151763263	AG04450	lung:	fetal
30	chr1:151763213-151763263	HL-60	blood:	n/a
31	chr1:151763213-151763263	SK-N-MC	brain:	n/a
32	chr1:151763213-151763263	ECC-1	luminal epithelium:	n/a
33	chr1:151763213-151763263	HCPEpiC	choroid plexus:	n/a
34	chr1:151763213-151763263	ovcar-3	ovarian:	n/a
35	chr1:151763213-151763263	BJ	skin:	n/a
36	chr1:151763213-151763263	HEEpiC	esophagus:	n/a
37	chr1:151763213-151763263	Jurkat	blood:	n/a
38	chr1:151763213-151763263	H1-hESC	embryonic stem cell:	embryo
39	chr1:151763213-151763263	HNPCEpiC	eye:	n/a
40	chr1:151763213-151763263	LNCaP	prostate:	n/a
41	chr1:151763213-151763263	U87	brain:	n/a
42	chr1:151763213-151763263	NHBE	bronchial:	n/a
43	chr1:151763213-151763263	HRCEpiC	kidney:	n/a
44	chr1:151763213-151763263	GM12878	blood:	n/a
45	chr1:151763213-151763263	PANC-1	pancreas:	n/a
46	chr1:151763213-151763263	AG10803	skin:	n/a
47	chr1:151763213-151763263	NHDF-neo	bronchial:	n/a
48	chr1:151763213-151763263	Hepatocyte	liver:	n/a
49	chr1:151763213-151763263	SKMC	muscle:	n/a
50	chr1:151763213-151763263	PrEC	prostate:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:151735509..151737891-chr1:151761737..151764631,3	K562	blood:
2	chr1:151732101..151733764-chr1:151763147..151765011,2	MCF-7	breast:
3	chr1:151760700..151764856-chr1:151797170..151799946,4	MCF-7	breast:
4	chr1:151511022..151513078-chr1:151762186..151764520,2	MCF-7	breast:
5	chr1:151736194..151739106-chr1:151761711..151764631,3	K562	blood:
6	chr1:151762059..151766604-chr1:151800169..151809078,15	MCF-7	breast:
7	chr1:151727449..151729119-chr1:151762483..151764442,2	K562	blood:
8	chr1:151740105..151741815-chr1:151762387..151764682,2	MCF-7	breast:
9	chr1:151042193..151044467-chr1:151761804..151763901,2	MCF-7	breast:
10	chr1:151733895..151739384-chr1:151759968..151766425,14	MCF-7	breast:
11	chr1:151739515..151742335-chr1:151761325..151763693,2	MCF-7	breast:
12	chr1:151583249..151586152-chr1:151761338..151763937,3	K562	blood:
13	chr1:151734278..151737585-chr1:151760529..151764689,8	MCF-7	breast:
14	chr1:151762360..151764432-chr1:151777142..151778868,2	MCF-7	breast:
15	chr1:151760926..151765128-chr1:151802888..151806720,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203288	TF binding region
TDRKH	TF binding region
ENSG00000203288	CpG island
TDRKH	CpG island
ENSG00000232937	Chromatin interaction
ENSG00000143458	Chromatin interaction
ENSG00000249602	Chromatin interaction
ENSG00000269621	Chromatin interaction
ENSG00000143365	Chromatin interaction
ENSG00000143376	Chromatin interaction
ENSG00000232536	Chromatin interaction
ENSG00000143436	Chromatin interaction
ENSG00000250734	Chromatin interaction
ENSG00000197622	Chromatin interaction
ENSG00000143450	Chromatin interaction
ENSG00000213171	Chromatin interaction
ENSG00000143367	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1054479	0.97[EUR][1000 genomes]
rs10788809	0.98[EUR][1000 genomes]
rs11204884	0.94[EUR][1000 genomes]
rs11204892	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11585294	0.99[EUR][1000 genomes]
rs11586946	0.99[EUR][1000 genomes]
rs11588258	0.82[EUR][1000 genomes]
rs11588634	0.82[EUR][1000 genomes]
rs11810571	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196456	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12238987	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1521185	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3790514	0.91[CEU][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs3811415	0.99[EUR][1000 genomes]
rs3811416	1.00[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4504897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4618976	0.99[EUR][1000 genomes]
rs4845356	1.00[EUR][1000 genomes]
rs4845570	1.00[EUR][1000 genomes]
rs4845575	0.83[AMR][1000 genomes]
rs4845579	0.94[ASW][hapmap];1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6659705	0.99[EUR][1000 genomes]
rs6664467	0.82[EUR][1000 genomes]
rs6673002	0.91[CEU][hapmap];0.93[TSI][hapmap];0.97[EUR][1000 genomes]
rs6673917	0.97[EUR][1000 genomes]
rs6681093	0.91[CEU][hapmap];0.93[TSI][hapmap];1.00[EUR][1000 genomes]
rs6683364	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs6694952	0.98[EUR][1000 genomes]
rs7416415	0.99[EUR][1000 genomes]
rs7542898	0.97[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010398	chr1:151761649-151790940	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3811414	PSMD4	cis	parietal	SCAN
rs3811414	CTSK	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:151761800-151764600	Active TSS	iPS-20b Cell Line	embryonic stem cell
2	chr1:151762000-151764200	Active TSS	Fetal Kidney	kidney
3	chr1:151762000-151764400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:151762000-151764400	Active TSS	Brain Germinal Matrix	brain
5	chr1:151762000-151764400	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr1:151762000-151764600	Active TSS	H1 Cell Line	embryonic stem cell
7	chr1:151762000-151764600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:151762200-151763800	Active TSS	Fetal Adrenal Gland	Adrenal Gland
9	chr1:151762200-151764000	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr1:151762200-151764000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr1:151762200-151764000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:151762200-151764000	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr1:151762200-151764000	Active TSS	Fetal Brain Female	brain
14	chr1:151762200-151764200	Active TSS	H9 Cell Line	embryonic stem cell
15	chr1:151762200-151764200	Active TSS	HUES64 Cell Line	embryonic stem cell
16	chr1:151762200-151764200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:151762200-151764400	Active TSS	ES-I3 Cell Line	embryonic stem cell
18	chr1:151762200-151764400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr1:151762200-151764400	Active TSS	HUES48 Cell Line	embryonic stem cell
20	chr1:151762200-151764400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr1:151762200-151764400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr1:151762200-151764400	Active TSS	Brain Angular Gyrus	brain
23	chr1:151762200-151764400	Active TSS	Brain Anterior Caudate	brain
24	chr1:151762200-151764400	Active TSS	A549	lung
25	chr1:151762200-151764400	Active TSS	HMEC	breast
26	chr1:151762200-151764600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr1:151762200-151764600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
28	chr1:151762200-151764600	Active TSS	Pancreatic Islets	Pancreatic Islet
29	chr1:151762400-151763400	Active TSS	Fetal Intestine Large	intestine
30	chr1:151762400-151763600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr1:151762400-151763800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr1:151762400-151763800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:151762400-151764000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr1:151762400-151764000	Active TSS	iPS-15b Cell Line	embryonic stem cell
35	chr1:151762400-151764000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
36	chr1:151762400-151764000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr1:151762400-151764000	Active TSS	Brain Substantia Nigra	brain
38	chr1:151762400-151764000	Bivalent/Poised TSS	Fetal Stomach	stomach
39	chr1:151762400-151764000	Active TSS	Left Ventricle	heart
40	chr1:151762400-151764000	Active TSS	Psoas Muscle	Psoas
41	chr1:151762400-151764000	Active TSS	Right Atrium	heart
42	chr1:151762400-151764000	Active TSS	HSMM	muscle
43	chr1:151762400-151764000	Active TSS	NHLF	lung
44	chr1:151762400-151764200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr1:151762400-151764200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr1:151762400-151764200	Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr1:151762400-151764200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr1:151762400-151764200	Flanking Active TSS	Primary B cells from cord blood	blood
49	chr1:151762400-151764200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr1:151762400-151764200	Active TSS	Colonic Mucosa	Colon

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