Variant report

Variant	rs3754417
Chromosome Location	chr1:226926006-226926007
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	POLR2A	chr1:226924813-226927292	GM18951	blood:	n/a	n/a
2	POLR2A	chr1:226925987-226926619	A549	lung:	n/a	n/a
3	EBF1	chr1:226924516-226926095	GM12878	blood:	n/a	n/a
4	POLR2A	chr1:226925497-226927787	GM12891	blood:	n/a	n/a
5	CTCF	chr1:226925920-226926070	HEK293	kidney:	n/a	n/a
6	ELF1	chr1:226924631-226926796	GM12878	blood:	n/a	chr1:226925320-226925332 chr1:226925234-226925246 chr1:226925181-226925190 chr1:226925207-226925216
7	STAT5A	chr1:226925269-226927371	GM12878	blood:	n/a	n/a
8	EBF1	chr1:226925461-226926061	GM12878	blood:	n/a	n/a
9	NFIC	chr1:226925913-226926383	GM12878	blood:	n/a	n/a
10	POLR2A	chr1:226924829-226927116	GM18526	blood:	n/a	n/a
11	MYC	chr1:226925854-226926509	NB4	blood:	n/a	n/a
12	MAX	chr1:226925440-226927069	GM12878	blood:	n/a	chr1:226925784-226925793
13	POLR2A	chr1:226925513-226927408	Raji	blood:	n/a	n/a
14	EP300	chr1:226925972-226926155	GM12878	blood:	n/a	n/a
15	RUNX3	chr1:226925350-226926152	GM12878	blood:	n/a	n/a
16	FOXA2	chr1:226925575-226926191	A549	lung:	n/a	n/a
17	MAX	chr1:226925422-226926552	SK-N-SH	brain:	n/a	chr1:226925784-226925793
18	CTCF	chr1:226925880-226926030	GM12874	blood:	n/a	n/a
19	CTCF	chr1:226925860-226926010	GM12865	blood:	n/a	n/a
20	TCF12	chr1:226925690-226926952	A549	lung:	n/a	chr1:226925766-226925775
21	POLR2A	chr1:226925364-226926096	GM12891	blood:	n/a	n/a
22	CTCF	chr1:226925808-226926010	GM19238	blood:	n/a	n/a
23	CTCF	chr1:226925856-226926015	MCF-7	breast:	n/a	n/a
24	CTBP2	chr1:226923487-226926606	H1-hESC	embryonic stem cell:	n/a	n/a
25	E2F6	chr1:226925654-226927236	A549	lung:	n/a	chr1:226926722-226926739 chr1:226926500-226926509 chr1:226926439-226926449 chr1:226926729-226926736 chr1:226926725-226926736
26	POLR2A	chr1:226925389-226926601	GM12878	blood:	n/a	n/a
27	MAX	chr1:226925543-226927309	A549	lung:	n/a	chr1:226925784-226925793
28	CHD1	chr1:226925707-226927587	GM12878	blood:	n/a	n/a
29	POLR2A	chr1:226925657-226927317	MCF10A-Er-Src	breast:	n/a	n/a
30	MYC	chr1:226925522-226926483	MCF10A-Er-Src	breast:	n/a	chr1:226925784-226925793
31	FOXA1	chr1:226925596-226926349	T-47D	breast:	n/a	n/a
32	POLR2A	chr1:226924979-226927504	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:226925942-226926597	MCF-7	breast:	n/a	n/a
34	MTA3	chr1:226925381-226927686	GM12878	blood:	n/a	n/a
35	RUNX3	chr1:226925975-226927685	GM12878	blood:	n/a	chr1:226927285-226927294 chr1:226927285-226927294
36	E2F6	chr1:226924527-226926414	H1-hESC	embryonic stem cell:	n/a	chr1:226925179-226925189 chr1:226925568-226925577 chr1:226925269-226925284 chr1:226925178-226925187 chr1:226925259-226925269 chr1:226925565-226925577
37	POLR2A	chr1:226924903-226927139	GM15510	blood:	n/a	n/a
38	GABPA	chr1:226925660-226926659	H1-hESC	embryonic stem cell:	n/a	chr1:226926204-226926213
39	CTCF	chr1:226925900-226926050	GM12864	blood:	n/a	n/a
40	MAX	chr1:226925772-226926583	NB4	blood:	n/a	chr1:226925784-226925793
41	CTCF	chr1:226925849-226926026	GM19240	blood:	n/a	n/a
42	MAX	chr1:226925375-226926679	SK-N-SH	brain:	n/a	chr1:226925784-226925793
43	SIN3AK20	chr1:226925627-226927307	MCF-7	breast:	n/a	n/a
44	ZNF263	chr1:226925841-226927278	HEK293-T-REx	kidney:	n/a	n/a
45	POLR2A	chr1:226925853-226926529	HUVEC	blood vessel:	n/a	n/a
46	SIN3A	chr1:226925481-226926575	GM12878	blood:	n/a	chr1:226926386-226926399 chr1:226925907-226925916
47	MAX	chr1:226925694-226926488	MCF-7	breast:	n/a	chr1:226925784-226925793
48	POLR2A	chr1:226925788-226927029	MCF10A-Er-Src	breast:	n/a	n/a
49	HDAC2	chr1:226925604-226926658	MCF-7	breast:	n/a	chr1:226926199-226926208 chr1:226925766-226925775
50	MAX	chr1:226925269-226926423	H1-hESC	embryonic stem cell:	n/a	chr1:226925784-226925793

Variant related genes	Relation type
ITPKB	TF binding region

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1124377	0.80[AMR][1000 genomes]
rs16846452	0.83[AMR][1000 genomes]
rs16846458	0.83[AMR][1000 genomes]
rs16846461	0.83[AMR][1000 genomes]
rs16846464	0.83[AMR][1000 genomes]
rs3754406	0.83[AMR][1000 genomes]
rs3754407	0.83[AMR][1000 genomes]
rs3754413	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3768397	0.83[AMR][1000 genomes]
rs3768400	0.83[AMR][1000 genomes]
rs3768416	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3820647	0.93[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4653464	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs56095953	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997468	chr1:226858660-226975311	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv535316	chr1:226858660-226975311	Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	esv3338179	chr1:226923854-226926702	Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Strong transcription	TF binding region CpG island	1 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	chr1:226920400-226927000	Transcr. at gene 5' and 3'	Primary T helper naive cells fromperipheralblood	blood
2	chr1:226920800-226927200	Active TSS	Psoas Muscle	Psoas
3	chr1:226921000-226927600	Active TSS	Right Atrium	heart
4	chr1:226922600-226927000	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
5	chr1:226922800-226927000	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
6	chr1:226923600-226927200	Active TSS	Left Ventricle	heart
7	chr1:226923800-226927200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
8	chr1:226923800-226927600	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
9	chr1:226924000-226927200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
10	chr1:226924000-226927400	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr1:226924200-226927000	Active TSS	Small Intestine	intestine
12	chr1:226924200-226927200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
13	chr1:226924200-226927200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:226924200-226927400	Active TSS	Duodenum Smooth Muscle	Duodenum
15	chr1:226924400-226927200	Active TSS	Right Ventricle	heart
16	chr1:226924400-226927400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
17	chr1:226924400-226927400	Active TSS	Rectal Mucosa Donor 29	rectum
18	chr1:226924400-226927600	Active TSS	Brain Angular Gyrus	brain
19	chr1:226924600-226926200	Active TSS	Fetal Brain Female	brain
20	chr1:226924600-226927000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr1:226924600-226927000	Active TSS	Sigmoid Colon	Sigmoid Colon
22	chr1:226924600-226927200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
23	chr1:226924600-226927200	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
24	chr1:226924600-226927400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr1:226924600-226927400	Active TSS	Brain Anterior Caudate	brain
26	chr1:226924600-226927400	Active TSS	Colon Smooth Muscle	Colon
27	chr1:226924600-226927400	Active TSS	Fetal Kidney	kidney
28	chr1:226924600-226927400	Active TSS	Rectal Smooth Muscle	rectum
29	chr1:226924600-226927400	Active TSS	NHDF-Ad	bronchial
30	chr1:226924600-226927600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr1:226924800-226926400	Flanking Active TSS	HMEC	breast
32	chr1:226924800-226926600	Bivalent/Poised TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr1:226924800-226927000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr1:226924800-226927000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr1:226924800-226927000	Bivalent/Poised TSS	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr1:226924800-226927000	Active TSS	Esophagus	oesophagus
37	chr1:226924800-226927000	Active TSS	Gastric	stomach
38	chr1:226924800-226927000	Active TSS	HSMM	muscle
39	chr1:226924800-226927200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr1:226924800-226927200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr1:226924800-226927200	Active TSS	Ovary	ovary
42	chr1:226924800-226927400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:226924800-226927400	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
44	chr1:226924800-226927400	Active TSS	Breast Myoepithelial Primary Cells	Breast
45	chr1:226924800-226927400	Active TSS	Primary T cells from cord blood	blood
46	chr1:226924800-226927400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
47	chr1:226924800-226927400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr1:226924800-226927400	Active TSS	Brain Cingulate Gyrus	brain
49	chr1:226924800-226927400	Active TSS	Brain Inferior Temporal Lobe	brain
50	chr1:226924800-226927400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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