Variant report

Variant	rs1996874
Chromosome Location	chr3:49453505-49453506
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	chr3:49453309-49453709	GM12878	blood:	n/a	n/a
2	EGR1	chr3:49453488-49453658	GM12878	blood:	n/a	chr3:49453567-49453581
3	POLR2A	chr3:49453022-49454928	GM12892	blood:	n/a	n/a
4	POLR2A	chr3:49452855-49454130	HepG2	liver:	n/a	n/a
5	POLR2A	chr3:49453106-49454137	GM12891	blood:	n/a	n/a
6	RELA	chr3:49453063-49454171	GM12891	blood:	n/a	n/a
7	RAD21	chr3:49452866-49453509	HCT-116	colon:	n/a	n/a
8	MTA3	chr3:49452886-49454772	GM12878	blood:	n/a	n/a
9	POLR2A	chr3:49453407-49453691	K562	blood:	n/a	n/a
10	POLR2A	chr3:49453504-49453548	HUVEC	blood vessel:	n/a	n/a
11	POLR2A	chr3:49453069-49454188	GM12891	blood:	n/a	n/a
12	PML	chr3:49453196-49454219	GM12878	blood:	n/a	n/a
13	ELF1	chr3:49453495-49454205	GM12878	blood:	n/a	chr3:49453894-49453907
14	POLR2A	chr3:49453196-49454088	GM12892	blood:	n/a	n/a
15	POLR2A	chr3:49453054-49454928	GM12891	blood:	n/a	n/a
16	RELA	chr3:49453108-49454094	GM15510	blood:	n/a	n/a
17	POLR2A	chr3:49453159-49454154	GM12891	blood:	n/a	n/a
18	POLR2A	chr3:49452978-49454414	GM12878	blood:	n/a	n/a
19	POLR2A	chr3:49453496-49454169	PFSK-1	brain:	n/a	n/a
20	POLR2A	chr3:49453369-49453811	GM12878	blood:	n/a	n/a
21	YY1	chr3:49453408-49453872	GM12891	blood:	n/a	n/a
22	EBF1	chr3:49453359-49454221	GM12878	blood:	n/a	chr3:49454043-49454052 chr3:49453990-49454001
23	ZEB1	chr3:49453244-49453695	GM12878	blood:	n/a	n/a
24	RUNX3	chr3:49453236-49454285	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:49452933-49454144	GM12892	blood:	n/a	n/a
26	RELA	chr3:49453132-49454084	GM19193	blood:	n/a	n/a
27	EP300	chr3:49453230-49454124	GM12878	blood:	n/a	chr3:49454039-49454055
28	PAX5	chr3:49453428-49454153	GM12878	blood:	n/a	n/a
29	MAX	chr3:49453190-49454013	GM12878	blood:	n/a	n/a
30	MAZ	chr3:49453432-49453616	GM12878	blood:	n/a	n/a
31	NFATC1	chr3:49453035-49454112	GM12878	blood:	n/a	n/a
32	POLR2A	chr3:49452801-49454197	GM12878	blood:	n/a	n/a
33	CTCF	chr3:49453360-49453510	GM12864	blood:	n/a	n/a
34	SPI1	chr3:49453479-49454342	HL-60	blood:	n/a	n/a
35	POU2F2	chr3:49453359-49454063	GM12891	blood:	n/a	n/a
36	ATF2	chr3:49453253-49454094	GM12878	blood:	n/a	n/a
37	POLR2A	chr3:49452993-49456018	HepG2	liver:	n/a	n/a
38	RAD21	chr3:49452999-49453681	GM12878	blood:	n/a	n/a
39	RELA	chr3:49453371-49454026	GM10847	blood:	n/a	n/a
40	RELA	chr3:49453036-49454101	GM19099	blood:	n/a	n/a
41	RELA	chr3:49453205-49454327	GM18951	blood:	n/a	n/a
42	POLR2A	chr3:49453055-49454791	GM12892	blood:	n/a	n/a
43	NFIC	chr3:49453360-49454176	GM12878	blood:	n/a	n/a
44	CEBPB	chr3:49453437-49453633	HepG2	liver:	n/a	n/a
45	ELK1	chr3:49453443-49453643	GM12878	blood:	n/a	n/a
46	EBF1	chr3:49453258-49454216	GM12878	blood:	n/a	chr3:49454043-49454052 chr3:49453990-49454001
47	EBF1	chr3:49453019-49454210	GM12878	blood:	n/a	chr3:49454043-49454052 chr3:49453990-49454001
48	FOXM1	chr3:49453443-49454197	GM12878	blood:	n/a	n/a
49	MTA3	chr3:49453360-49454349	GM12878	blood:	n/a	n/a
50	YY1	chr3:49453436-49453812	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:49453095..49455056-chr3:49457892..49460784,2	K562	blood:
2	chr3:49453314..49456247-chr3:49456435..49459274,2	MCF-7	breast:
3	chr3:49452077..49454427-chr3:49496570..49500540,3	MCF-7	breast:

Variant related genes	Relation type
RHOA	TF binding region
ENSG00000145020	Chromatin interaction
ENSG00000235261	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs11130197	1.00[YRI][hapmap]
rs11130201	0.84[AFR][1000 genomes]
rs11708174	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs11717485	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1522929	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1568663	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080495	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080510	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080567	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17080664	0.91[YRI][hapmap];0.87[AFR][1000 genomes]
rs2131107	0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2311794	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2311801	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2329024	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs28615670	1.00[EUR][1000 genomes]
rs3870334	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3870340	0.82[ASW][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs3912831	1.00[YRI][hapmap];1.00[EUR][1000 genomes]
rs4241409	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4452334	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4527417	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855856	1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855857	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855870	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs4855872	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs4855874	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855875	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855876	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855878	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4855879	1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55808753	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs55990645	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56101322	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56760510	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56897974	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59579780	0.81[AFR][1000 genomes]
rs60011446	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61749312	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446269	0.92[AFR][1000 genomes]
rs6446270	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446271	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446273	1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446276	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446278	0.88[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446279	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6446280	0.87[AFR][1000 genomes]
rs6446281	1.00[EUR][1000 genomes]
rs6446282	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs6446283	1.00[EUR][1000 genomes]
rs6762593	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs6766297	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6787665	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6793124	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6797164	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs72936890	1.00[EUR][1000 genomes]
rs73830703	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830704	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830705	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73830706	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73831434	1.00[EUR][1000 genomes]
rs73831435	1.00[EUR][1000 genomes]
rs73831436	1.00[EUR][1000 genomes]
rs73831437	1.00[EUR][1000 genomes]
rs73831438	1.00[EUR][1000 genomes]
rs73831439	0.81[AFR][1000 genomes]
rs73831440	0.81[AFR][1000 genomes]
rs73831441	0.81[AFR][1000 genomes]
rs73831442	0.87[AFR][1000 genomes]
rs7646393	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8179172	1.00[ASW][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9311441	0.95[AFR][1000 genomes]
rs9811460	1.00[EUR][1000 genomes]
rs9814413	1.00[EUR][1000 genomes]
rs9830627	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9837396	1.00[EUR][1000 genomes]
rs9849446	1.00[EUR][1000 genomes]
rs9861805	0.82[ASW][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9869504	1.00[EUR][1000 genomes]
rs9875203	1.00[AMR][1000 genomes];1.00[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	nsv834687	chr3:49448632-49631788	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:49450400-49459000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:49450400-49459400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:49450600-49453800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:49450600-49453800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr3:49450600-49454400	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr3:49450600-49454600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:49450600-49459000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr3:49450800-49453600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr3:49450800-49453800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
10	chr3:49450800-49454000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr3:49450800-49454200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr3:49450800-49454400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
13	chr3:49450800-49455400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr3:49450800-49457800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:49450800-49459000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr3:49450800-49459200	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr3:49450800-49459200	Genic enhancers	Placenta	Placenta
18	chr3:49451000-49453600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr3:49451000-49454400	Weak transcription	Fetal Kidney	kidney
20	chr3:49451000-49458000	Weak transcription	Small Intestine	intestine
21	chr3:49451200-49455000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr3:49451200-49459000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr3:49451200-49459400	Weak transcription	Fetal Brain Male	brain
24	chr3:49451200-49466200	Weak transcription	Psoas Muscle	Psoas
25	chr3:49451400-49453600	Weak transcription	Fetal Lung	lung
26	chr3:49451400-49454200	Weak transcription	K562	blood
27	chr3:49451400-49454600	Weak transcription	Fetal Heart	heart
28	chr3:49451400-49459400	Weak transcription	Ovary	ovary
29	chr3:49451600-49454600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr3:49451600-49458000	Strong transcription	NHLF	lung
31	chr3:49451600-49458200	Strong transcription	Fetal Intestine Small	intestine
32	chr3:49451800-49455600	Genic enhancers	Fetal Muscle Trunk	muscle
33	chr3:49452000-49453600	Genic enhancers	Primary T cells from cord blood	blood
34	chr3:49452000-49453800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:49452000-49454000	Strong transcription	A549	lung
36	chr3:49452000-49454200	Genic enhancers	Duodenum Mucosa	Duodenum
37	chr3:49452000-49454800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
38	chr3:49452000-49455000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr3:49452000-49455000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:49452000-49455000	Strong transcription	Placenta Amnion	Placenta Amnion
41	chr3:49452000-49455200	Strong transcription	Brain Germinal Matrix	brain
42	chr3:49452000-49455400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr3:49452000-49455400	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:49452000-49455400	Strong transcription	Osteobl	bone
45	chr3:49452000-49457400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr3:49452000-49458200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr3:49452200-49453600	Genic enhancers	Brain Hippocampus Middle	brain
48	chr3:49452200-49453600	Strong transcription	Rectal Smooth Muscle	rectum
49	chr3:49452200-49453800	Genic enhancers	Left Ventricle	heart
50	chr3:49452200-49453800	Genic enhancers	Stomach Mucosa	stomach

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