Variant report

Variant	rs41379148
Chromosome Location	chr2:46930169-46930170
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46925096..46927639-chr2:46929889..46935400,5	MCF-7	breast:
2	chr2:46930002..46931505-chr2:46938996..46941968,2	K562	blood:
3	chr2:46929305..46931756-chr2:46933052..46934727,2	MCF-7	breast:
4	chr2:46924915..46928636-chr2:46928946..46932522,6	MCF-7	breast:
5	chr2:46930029..46933528-chr2:46976256..46980348,3	K562	blood:

Variant related genes	Relation type
ENSG00000171150	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10495937	0.95[EUR][1000 genomes]
rs11903382	0.87[EUR][1000 genomes]
rs1446496	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1446497	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1446498	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17767307	1.00[AFR][1000 genomes]
rs17769580	0.80[EUR][1000 genomes]
rs17769689	0.80[EUR][1000 genomes]
rs17771005	0.92[EUR][1000 genomes]
rs17771017	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17771098	0.88[EUR][1000 genomes]
rs17771201	0.88[EUR][1000 genomes]
rs17771237	0.87[EUR][1000 genomes]
rs17771255	0.87[EUR][1000 genomes]
rs17771357	0.87[EUR][1000 genomes]
rs17771942	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772285	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17772991	1.00[AFR][1000 genomes]
rs17820969	0.82[EUR][1000 genomes]
rs17821218	0.82[EUR][1000 genomes]
rs17821989	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17822782	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2045290	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3927078	0.80[EUR][1000 genomes]
rs41371146	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs55874432	0.91[EUR][1000 genomes]
rs55928499	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56006635	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56199036	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56224128	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs56800355	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57124017	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs58903656	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6731970	0.93[EUR][1000 genomes]
rs6735101	0.92[EUR][1000 genomes]
rs72800535	1.00[AFR][1000 genomes]
rs72800543	1.00[AFR][1000 genomes]
rs72800550	1.00[AFR][1000 genomes]
rs72800587	0.80[EUR][1000 genomes]
rs72800597	0.82[EUR][1000 genomes]
rs72800599	0.82[EUR][1000 genomes]
rs72800600	0.82[EUR][1000 genomes]
rs72800602	0.82[EUR][1000 genomes]
rs72802404	0.82[EUR][1000 genomes]
rs72802406	0.82[EUR][1000 genomes]
rs72802407	0.85[EUR][1000 genomes]
rs72802408	0.82[EUR][1000 genomes]
rs72802411	0.81[EUR][1000 genomes]
rs72802415	1.00[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs72802420	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802426	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802428	0.84[EUR][1000 genomes]
rs72802429	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72802430	1.00[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs72802435	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs72802441	0.93[EUR][1000 genomes]
rs72802444	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802445	0.82[EUR][1000 genomes]
rs72802448	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802451	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802454	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802455	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802456	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802458	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72802463	0.93[EUR][1000 genomes]
rs72802466	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802467	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802486	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802487	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72802492	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs72802498	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7566275	0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
2	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv533112	chr2:46800828-46959977	Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv817517	chr2:46819371-47715140	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
6	nsv873997	chr2:46821640-46984627	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46925800-46930200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr2:46925800-46930200	Active TSS	NHLF	lung
3	chr2:46927200-46935800	Weak transcription	Spleen	Spleen
4	chr2:46927400-46931400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:46927400-46932000	Weak transcription	Gastric	stomach
6	chr2:46927400-46932000	Weak transcription	Pancreas	Pancrea
7	chr2:46927400-46933400	Weak transcription	Brain Angular Gyrus	brain
8	chr2:46927400-46933800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr2:46927600-46930600	Enhancers	Small Intestine	intestine
10	chr2:46927600-46930800	Weak transcription	Colonic Mucosa	Colon
11	chr2:46927600-46931400	Weak transcription	Brain Hippocampus Middle	brain
12	chr2:46927600-46931600	Weak transcription	Stomach Mucosa	stomach
13	chr2:46927600-46932800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:46927800-46930600	Enhancers	Fetal Lung	lung
15	chr2:46927800-46931000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr2:46927800-46931000	Weak transcription	Monocytes-CD14+_RO01746	blood
17	chr2:46927800-46940000	Weak transcription	Primary hematopoietic stem cells	blood
18	chr2:46928000-46931000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:46928000-46931000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:46928000-46931200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr2:46928000-46931800	Weak transcription	Aorta	Aorta
22	chr2:46928000-46931800	Weak transcription	Fetal Muscle Leg	muscle
23	chr2:46928000-46943600	Weak transcription	Thymus	Thymus
24	chr2:46928400-46931000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
25	chr2:46928400-46932200	Weak transcription	HSMM	muscle
26	chr2:46928600-46930600	Enhancers	H1 Cell Line	embryonic stem cell
27	chr2:46928600-46930600	Weak transcription	Primary B cells from cord blood	blood
28	chr2:46928600-46931000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr2:46928600-46931600	Weak transcription	Brain Cingulate Gyrus	brain
30	chr2:46928600-46932400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr2:46928600-46933600	Weak transcription	Brain Substantia Nigra	brain
32	chr2:46928600-46933600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:46928600-46934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr2:46928600-46944400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr2:46928800-46930200	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr2:46928800-46930400	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr2:46928800-46930400	Weak transcription	Primary T cells from cord blood	blood
38	chr2:46928800-46930600	Enhancers	HUES64 Cell Line	embryonic stem cell
39	chr2:46928800-46931000	Enhancers	iPS-15b Cell Line	embryonic stem cell
40	chr2:46928800-46931000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:46928800-46931600	Weak transcription	Stomach Smooth Muscle	stomach
42	chr2:46928800-46932000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr2:46928800-46932000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr2:46928800-46932000	Weak transcription	Left Ventricle	heart
45	chr2:46928800-46932200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr2:46928800-46932400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:46928800-46932400	Weak transcription	HUVEC	blood vessel
48	chr2:46928800-46932600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:46928800-46932600	Weak transcription	Placenta Amnion	Placenta Amnion
50	chr2:46928800-46932600	Enhancers	HepG2	liver

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