Variant report

Variant	rs2232249
Chromosome Location	chr3:50614361-50614362
allele	G/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	chr3:50614359-50614443	HepG2	liver:	n/a	n/a
2	POLR2A	chr3:50614348-50614463	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:50613663..50623986-chr3:50635558..50652363,41	MCF-7	breast:
2	chr3:50608156..50612219-chr3:50612794..50616407,4	K562	blood:
3	chr3:50613912..50618382-chr3:50647156..50650083,6	K562	blood:
4	chr3:50606526..50611586-chr3:50612274..50616724,6	MCF-7	breast:

Variant related genes	Relation type
HEMK1	TF binding region
ENSG00000088543	Chromatin interaction
ENSG00000114735	Chromatin interaction
ENSG00000114738	Chromatin interaction
ENSG00000114737	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs13321914	1.00[AMR][1000 genomes]
rs17050997	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051020	1.00[AMR][1000 genomes]
rs17051027	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051036	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17051472	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2085581	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2232252	1.00[AMR][1000 genomes]
rs2355324	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs2355336	1.00[AFR][1000 genomes]
rs28496515	1.00[AMR][1000 genomes]
rs28525150	1.00[AMR][1000 genomes]
rs28546448	1.00[AMR][1000 genomes]
rs736472	1.00[AMR][1000 genomes]
rs751850	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs762893	1.00[AMR][1000 genomes]
rs762894	1.00[AMR][1000 genomes]
rs9822071	1.00[AMR][1000 genomes]
rs9832171	1.00[AMR][1000 genomes]
rs9841390	1.00[AMR][1000 genomes]
rs9841986	1.00[AMR][1000 genomes]
rs9850032	1.00[AMR][1000 genomes]
rs9866852	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
3	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
5	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
8	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
9	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50607400-50615600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:50607400-50628200	Weak transcription	Small Intestine	intestine
3	chr3:50607600-50614400	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr3:50607600-50617600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:50607600-50628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr3:50607800-50614800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr3:50607800-50615200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:50607800-50615200	Weak transcription	Aorta	Aorta
9	chr3:50607800-50620000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr3:50607800-50628200	Weak transcription	HSMMtube	muscle
11	chr3:50607800-50628600	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr3:50608000-50618400	Weak transcription	NH-A	brain
13	chr3:50608000-50621400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr3:50608000-50621400	Weak transcription	HUVEC	blood vessel
15	chr3:50608000-50621800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr3:50608200-50614400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr3:50608200-50615200	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr3:50608200-50616200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr3:50608200-50617400	Weak transcription	Fetal Brain Male	brain
20	chr3:50608200-50624000	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr3:50608200-50628400	Weak transcription	A549	lung
22	chr3:50608200-50637400	Weak transcription	Fetal Kidney	kidney
23	chr3:50608400-50614800	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:50608400-50615000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr3:50608400-50625600	Weak transcription	NHDF-Ad	bronchial
26	chr3:50608800-50614800	Genic enhancers	Placenta	Placenta
27	chr3:50609200-50620800	Strong transcription	Brain Germinal Matrix	brain
28	chr3:50609800-50620600	Strong transcription	Fetal Brain Female	brain
29	chr3:50610000-50614400	Weak transcription	Primary B cells from cord blood	blood
30	chr3:50610000-50621400	Weak transcription	Primary neutrophils fromperipheralblood	blood
31	chr3:50610000-50623000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
32	chr3:50610200-50614400	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr3:50610200-50615200	Weak transcription	Left Ventricle	heart
34	chr3:50610200-50618000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
35	chr3:50610200-50618800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr3:50610200-50620400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr3:50610200-50623600	Strong transcription	Fetal Muscle Leg	muscle
38	chr3:50610200-50624400	Strong transcription	Fetal Stomach	stomach
39	chr3:50610200-50628000	Weak transcription	Stomach Mucosa	stomach
40	chr3:50610400-50614400	Weak transcription	Right Ventricle	heart
41	chr3:50610400-50614600	Enhancers	Primary T helper naive cells from peripheral blood	blood
42	chr3:50610400-50615600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
43	chr3:50610400-50618600	Weak transcription	Right Atrium	heart
44	chr3:50610400-50622400	Weak transcription	GM12878-XiMat	blood
45	chr3:50610400-50623200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:50610400-50623200	Strong transcription	Stomach Smooth Muscle	stomach
47	chr3:50610400-50628400	Weak transcription	HSMM	muscle
48	chr3:50610600-50615200	Enhancers	K562	blood
49	chr3:50610600-50616000	Strong transcription	Brain Cingulate Gyrus	brain
50	chr3:50610600-50618200	Strong transcription	Adipose Nuclei	Adipose

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