Variant report

Variant	rs61459154
Chromosome Location	chr1:226190329-226190330
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	POLR2A	chr1:226189695-226190520	GM12878	blood:	n/a	n/a
2	SPI1	chr1:226189689-226190418	GM12891	blood:	n/a	chr1:226189944-226189957
3	POLR2A	chr1:226189911-226190856	GM15510	blood:	n/a	n/a
4	STAT1	chr1:226189767-226190686	Hela-S3	cervix:	n/a	chr1:226190026-226190034 chr1:226190631-226190643 chr1:226190000-226190011
5	MAX	chr1:226189690-226190923	K562	blood:	n/a	chr1:226189896-226189906 chr1:226190635-226190645 chr1:226189931-226189941
6	ZC3H11A	chr1:226190114-226191031	K562	blood:	n/a	n/a
7	CEBPD	chr1:226189783-226191178	K562	blood:	n/a	n/a
8	STAT3	chr1:226189400-226190335	MCF10A-Er-Src	breast:	n/a	chr1:226190140-226190161 chr1:226190026-226190034 chr1:226189663-226189671
9	KAP1	chr1:226190117-226190489	K562	blood:	n/a	n/a
10	IKZF1	chr1:226189651-226190588	GM12878	blood:	n/a	n/a
11	CEBPD	chr1:226189727-226191207	K562	blood:	n/a	n/a
12	POLR2A	chr1:226189785-226190979	K562	blood:	n/a	n/a
13	MAFK	chr1:226189941-226190977	K562	blood:	n/a	n/a
14	MAFF	chr1:226189752-226191251	K562	blood:	n/a	n/a
15	ELK1	chr1:226190165-226190928	K562	blood:	n/a	n/a
16	SPI1	chr1:226189760-226190453	GM12891	blood:	n/a	chr1:226189944-226189957
17	POLR2A	chr1:226189603-226191009	H1-neurons	neurons:	n/a	n/a
18	POLR2A	chr1:226189672-226190970	K562	blood:	n/a	n/a
19	ZNF143	chr1:226189419-226190967	K562	blood:	n/a	n/a
20	POLR2A	chr1:226190319-226190815	HCT-116	colon:	n/a	n/a
21	WRNIP1	chr1:226189765-226190546	GM12878	blood:	n/a	n/a
22	RUNX3	chr1:226189629-226190452	GM12878	blood:	n/a	n/a
23	MYC	chr1:226189669-226191208	K562	blood:	n/a	chr1:226189896-226189906 chr1:226190635-226190645 chr1:226189931-226189941
24	TAF1	chr1:226189734-226190928	H1-neurons	neurons:	n/a	n/a
25	RELA	chr1:226189766-226190596	GM19099	blood:	n/a	n/a
26	ATF2	chr1:226189592-226190554	GM12878	blood:	n/a	n/a
27	TAF1	chr1:226189678-226190966	H1-neurons	neurons:	n/a	n/a
28	USF2	chr1:226189772-226190483	K562	blood:	n/a	n/a
29	POLR2A	chr1:226189678-226190958	K562	blood:	n/a	n/a
30	BHLHE40	chr1:226189667-226190980	K562	blood:	n/a	n/a
31	POLR2A	chr1:226189734-226190924	GM12891	blood:	n/a	n/a
32	MTA3	chr1:226189542-226190847	GM12878	blood:	n/a	n/a
33	POLR2A	chr1:226189614-226190993	PBDE	blood:	n/a	n/a
34	JUN	chr1:226188614-226191131	K562	blood:	n/a	chr1:226190415-226190427 chr1:226189662-226189671 chr1:226189874-226189883
35	STAT5A	chr1:226190206-226191139	K562	blood:	n/a	chr1:226190631-226190643
36	KAP1	chr1:226189668-226190910	HEK293	kidney:	n/a	n/a
37	POLR2A	chr1:226189767-226190839	HUVEC	blood vessel:	n/a	n/a
38	JUND	chr1:226189670-226191040	K562	blood:	n/a	chr1:226190415-226190427 chr1:226189874-226189883
39	TBL1XR1	chr1:226189616-226190372	GM12878	blood:	n/a	n/a
40	POLR2A	chr1:226189723-226190962	K562	blood:	n/a	n/a
41	EP300	chr1:226189494-226191225	K562	blood:	n/a	chr1:226189588-226189602
42	E2F6	chr1:226189716-226190911	K562	blood:	n/a	chr1:226189875-226189884 chr1:226189873-226189882
43	BACH1	chr1:226190264-226190939	K562	blood:	n/a	n/a
44	POLR2A	chr1:226190329-226190890	K562	blood:	n/a	n/a
45	STAT3	chr1:226189751-226190339	MCF10A-Er-Src	breast:	n/a	chr1:226190140-226190161 chr1:226190026-226190034
46	MYC	chr1:226190111-226190335	HUVEC	blood vessel:	n/a	n/a
47	CTCF	chr1:226190220-226190370	K562	blood:	n/a	n/a
48	BHLHE40	chr1:226189718-226190349	HepG2	liver:	n/a	n/a
49	MTA3	chr1:226189639-226190421	GM12878	blood:	n/a	n/a
50	POLR2A	chr1:226189557-226191009	H1-neurons	neurons:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:226148548..226150301-chr1:226188144..226190996,2	K562	blood:
2	chr1:226188590..226191989-chr1:226218669..226223499,6	K562	blood:
3	chr1:226183087..226192322-chr1:226243551..226254243,95	K562	blood:
4	chr1:226190304..226192131-chr1:226220799..226223499,3	K562	blood:
5	chr1:226187874..226190820-chr1:226213394..226216312,2	K562	blood:
6	chr1:226110464..226115809-chr1:226185735..226190763,7	K562	blood:
7	chr1:226183029..226192481-chr1:226247725..226253108,31	MCF-7	breast:
8	chr1:226188843..226191078-chr1:226237826..226239830,2	K562	blood:
9	chr1:226184876..226191468-chr1:226247585..226254254,12	MCF-7	breast:
10	chr1:226188139..226192155-chr1:226228386..226234051,6	K562	blood:
11	chr1:226178791..226193771-chr1:226246813..226256535,111	K562	blood:
12	chr1:226187840..226190663-chr1:226296821..226299236,2	MCF-7	breast:
13	chr1:226108702..226117785-chr1:226183554..226190529,14	K562	blood:
14	chr1:226185796..226188880-chr1:226188906..226190706,6	MCF-7	breast:

Variant related genes	Relation type
SDE2	TF binding region
ENSG00000143811	Chromatin interaction
ENSG00000143751	Chromatin interaction
ENSG00000163041	Chromatin interaction
ENSG00000272562	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2755096	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2755098	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2816322	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2816325	0.81[AFR][1000 genomes]
rs6664668	0.90[AMR][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	esv1834948	chr1:225874059-226214882	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv524126	chr1:225973777-226210653	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	esv2762223	chr1:226025175-226201716	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' 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	39 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:226187400-226191000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
2	chr1:226187800-226190400	Weak transcription	Fetal Intestine Large	intestine
3	chr1:226187800-226190400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr1:226187800-226191000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:226188000-226190800	Enhancers	Stomach Mucosa	stomach
6	chr1:226188000-226198600	Weak transcription	Fetal Intestine Small	intestine
7	chr1:226188200-226190800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:226188200-226191000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
9	chr1:226188200-226191000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr1:226188200-226192600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr1:226188200-226192800	Enhancers	Primary B cells from peripheral blood	blood
12	chr1:226188200-226192800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr1:226188200-226193000	Enhancers	Primary T cells fromperipheralblood	blood
14	chr1:226188200-226195400	Weak transcription	Right Atrium	heart
15	chr1:226188400-226190400	Enhancers	Primary T cells from cord blood	blood
16	chr1:226188400-226192600	Enhancers	Fetal Thymus	thymus
17	chr1:226188600-226191000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr1:226188800-226190400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr1:226188800-226190800	Flanking Active TSS	Primary B cells from cord blood	blood
20	chr1:226188800-226190800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr1:226189000-226191000	Enhancers	Placenta	Placenta
22	chr1:226189000-226191000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
23	chr1:226189200-226190800	Enhancers	A549	lung
24	chr1:226189400-226190400	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr1:226189400-226190800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr1:226189400-226190800	Enhancers	Brain Inferior Temporal Lobe	brain
27	chr1:226189400-226191000	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr1:226189600-226190400	Flanking Active TSS	Duodenum Mucosa	Duodenum
29	chr1:226189600-226190800	Enhancers	Hela-S3	cervix
30	chr1:226189600-226191000	Flanking Active TSS	K562	blood
31	chr1:226189800-226190600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:226189800-226190600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:226189800-226190600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:226189800-226190600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
35	chr1:226189800-226190600	Enhancers	Skeletal Muscle Male	skeletal muscle
36	chr1:226189800-226190600	Enhancers	Dnd41	blood
37	chr1:226189800-226190600	Flanking Active TSS	GM12878-XiMat	blood
38	chr1:226189800-226190600	Enhancers	HSMM	muscle
39	chr1:226189800-226190600	Enhancers	HSMMtube	muscle
40	chr1:226189800-226190600	Flanking Active TSS	HUVEC	blood vessel
41	chr1:226189800-226190600	Enhancers	NHEK	skin
42	chr1:226189800-226190800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr1:226189800-226190800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr1:226189800-226190800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr1:226189800-226190800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
46	chr1:226189800-226190800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr1:226189800-226190800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:226189800-226190800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr1:226189800-226190800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:226189800-226190800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links