Variant report

Variant	rs3811416
Chromosome Location	chr1:151763815-151763816
allele	C/T
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	CHD2	chr1:151763771-151764163	Hela-S3	cervix:	n/a	chr1:151763978-151763987
2	HDAC2	chr1:151762308-151764216	MCF-7	breast:	n/a	n/a
3	PML	chr1:151762413-151763851	MCF-7	breast:	n/a	n/a
4	SIN3AK20	chr1:151762260-151764320	MCF-7	breast:	n/a	n/a
5	RCOR1	chr1:151762583-151764112	K562	blood:	n/a	n/a
6	MTA3	chr1:151763144-151763842	GM12878	blood:	n/a	n/a
7	POLR2A	chr1:151762481-151764180	H1-neurons	neurons:	n/a	n/a
8	ZBTB7A	chr1:151763500-151763965	ECC-1	luminal epithelium:	n/a	n/a
9	CHD2	chr1:151762742-151764174	HepG2	liver:	n/a	chr1:151763978-151763987
10	POLR2A	chr1:151762535-151764115	H1-neurons	neurons:	n/a	n/a
11	ELF1	chr1:151762380-151764190	MCF-7	breast:	n/a	chr1:151763877-151763886
12	RCOR1	chr1:151762087-151764336	IMR90	lung:	n/a	n/a
13	CHD1	chr1:151763756-151763944	GM12878	blood:	n/a	n/a
14	MAX	chr1:151762511-151764019	HepG2	liver:	n/a	chr1:151763829-151763839
15	SIN3AK20	chr1:151762238-151764160	MCF-7	breast:	n/a	n/a
16	ELF1	chr1:151762525-151764085	MCF-7	breast:	n/a	chr1:151763877-151763886
17	MAX	chr1:151762096-151764240	MCF-7	breast:	n/a	chr1:151763829-151763839
18	REST	chr1:151762364-151764219	H1-neurons	neurons:	n/a	chr1:151763910-151763917
19	HCFC1	chr1:151762293-151763862	Hela-S3	cervix:	n/a	n/a
20	SP1	chr1:151762629-151763825	A549	lung:	n/a	chr1:151763816-151763825 chr1:151763004-151763013 chr1:151763169-151763190 chr1:151763004-151763013 chr1:151763003-151763015 chr1:151763005-151763014
21	EGR1	chr1:151762432-151764195	MCF-7	breast:	n/a	chr1:151763006-151763016 chr1:151763006-151763019 chr1:151763828-151763838 chr1:151763007-151763017 chr1:151762603-151762616 chr1:151763006-151763019 chr1:151763005-151763020 chr1:151762946-151762960 chr1:151763007-151763017 chr1:151763847-151763857 chr1:151763006-151763019 chr1:151763006-151763019 chr1:151763816-151763831 chr1:151763007-151763016 chr1:151763007-151763018 chr1:151763005-151763019
22	ZBTB33	chr1:151763690-151764161	SK-N-SH	brain:	n/a	chr1:151763979-151763989 chr1:151763973-151763988
23	CHD2	chr1:151763791-151764141	H1-hESC	embryonic stem cell:	n/a	chr1:151763978-151763987
24	RFX5	chr1:151760827-151765002	SK-N-SH	brain:	n/a	chr1:151761465-151761474
25	GABPA	chr1:151762315-151764142	MCF-7	breast:	n/a	chr1:151763005-151763014
26	SIN3A	chr1:151762371-151764107	H1-hESC	embryonic stem cell:	n/a	n/a
27	ZBTB7A	chr1:151763597-151764145	K562	blood:	n/a	n/a
28	POLR2A	chr1:151762551-151764173	MCF-7	breast:	n/a	n/a
29	MXI1	chr1:151761776-151764760	SK-N-SH	brain:	n/a	n/a
30	CHD2	chr1:151763803-151764155	GM12878	blood:	n/a	chr1:151763978-151763987
31	POLR2A	chr1:151763801-151764052	HepG2	liver:	n/a	n/a
32	MXI1	chr1:151762624-151764103	HepG2	liver:	n/a	n/a
33	UBTF	chr1:151763504-151764075	K562	blood:	n/a	n/a
34	MAX	chr1:151762518-151764162	HepG2	liver:	n/a	chr1:151763829-151763839
35	CHD2	chr1:151762731-151764196	K562	blood:	n/a	chr1:151763978-151763987
36	MAX	chr1:151762435-151763819	MCF-7	breast:	n/a	n/a
37	POLR2A	chr1:151762550-151764119	MCF-7	breast:	n/a	n/a
38	E2F6	chr1:151762489-151764058	K562	blood:	n/a	chr1:151763005-151763014 chr1:151763053-151763062 chr1:151763743-151763753 chr1:151763729-151763738 chr1:151763002-151763014

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	chr1:151583249..151586152-chr1:151761338..151763937,3	K562	blood:
12	chr1:151734278..151737585-chr1:151760529..151764689,8	MCF-7	breast:
13	chr1:151762360..151764432-chr1:151777142..151778868,2	MCF-7	breast:
14	chr1:151760926..151765128-chr1:151802888..151806720,6	MCF-7	breast:

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

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[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	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1196456	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12238987	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1521185	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3790514	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs3811414	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]
rs3811415	0.99[EUR][1000 genomes]
rs4504897	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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];0.81[ASN][1000 genomes]
rs4845579	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6659705	0.99[EUR][1000 genomes]
rs6664467	0.82[EUR][1000 genomes]
rs6673002	0.91[CEU][hapmap];0.97[EUR][1000 genomes]
rs6673917	0.97[EUR][1000 genomes]
rs6681093	0.91[CEU][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

No data

Chromatin state (count:126 , 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	chr1:151762200-151764000	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:151762200-151764000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:151762200-151764000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:151762200-151764000	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr1:151762200-151764000	Active TSS	Fetal Brain Female	brain
13	chr1:151762200-151764200	Active TSS	H9 Cell Line	embryonic stem cell
14	chr1:151762200-151764200	Active TSS	HUES64 Cell Line	embryonic stem cell
15	chr1:151762200-151764200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr1:151762200-151764400	Active TSS	ES-I3 Cell Line	embryonic stem cell
17	chr1:151762200-151764400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr1:151762200-151764400	Active TSS	HUES48 Cell Line	embryonic stem cell
19	chr1:151762200-151764400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr1:151762200-151764400	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr1:151762200-151764400	Active TSS	Brain Angular Gyrus	brain
22	chr1:151762200-151764400	Active TSS	Brain Anterior Caudate	brain
23	chr1:151762200-151764400	Active TSS	A549	lung
24	chr1:151762200-151764400	Active TSS	HMEC	breast
25	chr1:151762200-151764600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr1:151762200-151764600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
27	chr1:151762200-151764600	Active TSS	Pancreatic Islets	Pancreatic Islet
28	chr1:151762400-151764000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr1:151762400-151764000	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr1:151762400-151764000	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:151762400-151764000	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr1:151762400-151764000	Active TSS	Brain Substantia Nigra	brain
33	chr1:151762400-151764000	Bivalent/Poised TSS	Fetal Stomach	stomach
34	chr1:151762400-151764000	Active TSS	Left Ventricle	heart
35	chr1:151762400-151764000	Active TSS	Psoas Muscle	Psoas
36	chr1:151762400-151764000	Active TSS	Right Atrium	heart
37	chr1:151762400-151764000	Active TSS	HSMM	muscle
38	chr1:151762400-151764000	Active TSS	NHLF	lung
39	chr1:151762400-151764200	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr1:151762400-151764200	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr1:151762400-151764200	Active TSS	iPS-18 Cell Line	embryonic stem cell
42	chr1:151762400-151764200	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr1:151762400-151764200	Flanking Active TSS	Primary B cells from cord blood	blood
44	chr1:151762400-151764200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr1:151762400-151764200	Active TSS	Colonic Mucosa	Colon
46	chr1:151762400-151764200	Active TSS	Esophagus	oesophagus
47	chr1:151762400-151764200	Active TSS	Fetal Heart	heart
48	chr1:151762400-151764200	Active TSS	Stomach Mucosa	stomach
49	chr1:151762400-151764400	Active TSS	Brain Cingulate Gyrus	brain
50	chr1:151762400-151764400	Active TSS	Brain Hippocampus Middle	brain

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