Variant report

Variant	rs4144242
Chromosome Location	chr15:41006987-41006988
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:41006871..41009134-chr15:41015963..41018302,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM82A2-1	chr15:41006211-41008592	ENSG00000245312

Extended variants
information (count: 24 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs1801320	0.89[CHB][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2304579	0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs45455000	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45503494	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45504895	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45507396	0.96[EUR][1000 genomes]
rs45559631	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs45579836	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs45585734	0.96[EUR][1000 genomes]
rs5030786	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs57736474	0.82[AMR][1000 genomes]
rs57936990	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58458955	0.91[EUR][1000 genomes]
rs59654927	0.91[EUR][1000 genomes]
rs60408076	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs61381741	0.91[EUR][1000 genomes]
rs73396510	0.85[ASN][1000 genomes]
rs73396515	0.85[ASN][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	nsv1053173	chr15:40933163-41094127	Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv542363	chr15:40933163-41094127	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv904099	chr15:40949526-41041875	Genic enhancers Enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
4	nsv529030	chr15:40956471-41012695	Active TSS Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv904101	chr15:40979651-41275014	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
6	nsv527234	chr15:40987725-41031686	Transcr. at gene 5' and 3' Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40988000-41030000	Weak transcription	Pancreas	Pancrea
2	chr15:40988200-41028600	Weak transcription	Spleen	Spleen
3	chr15:40988400-41020600	Weak transcription	Placenta	Placenta
4	chr15:40988400-41020800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr15:40988400-41021600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:40988400-41021800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:40988400-41027200	Weak transcription	Primary B cells from cord blood	blood
8	chr15:40988400-41031000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:40988600-41007800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:40988600-41018400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr15:40988600-41021400	Weak transcription	Duodenum Mucosa	Duodenum
12	chr15:40988600-41021400	Weak transcription	Fetal Brain Female	brain
13	chr15:40988800-41020600	Weak transcription	Primary T cells from cord blood	blood
14	chr15:40988800-41021600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr15:40988800-41021800	Weak transcription	Fetal Kidney	kidney
16	chr15:40989000-41012000	Weak transcription	NHLF	lung
17	chr15:40989000-41018000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40990200-41013200	Strong transcription	H1 Cell Line	embryonic stem cell
19	chr15:40990200-41016800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr15:40990200-41016800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr15:40990600-41015000	Strong transcription	HUES64 Cell Line	embryonic stem cell
22	chr15:40990600-41022600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:40990800-41016000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
24	chr15:40991000-41007200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr15:40992000-41016600	Strong transcription	Dnd41	blood
26	chr15:40993200-41025800	Weak transcription	Placenta Amnion	Placenta Amnion
27	chr15:40994000-41020600	Weak transcription	HSMM	muscle
28	chr15:40997800-41020800	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:40998200-41023200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr15:40998400-41007000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr15:40998800-41038000	Weak transcription	Stomach Mucosa	stomach
32	chr15:40999000-41011600	Weak transcription	Fetal Intestine Large	intestine
33	chr15:40999000-41027600	Weak transcription	Gastric	stomach
34	chr15:40999200-41021600	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr15:41000000-41026000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr15:41000400-41007400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:41000400-41008000	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr15:41001000-41008400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr15:41001400-41020800	Weak transcription	NHDF-Ad	bronchial
40	chr15:41001600-41020600	Weak transcription	NH-A	brain
41	chr15:41002000-41019600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:41002000-41021400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:41002200-41007800	Weak transcription	Fetal Muscle Leg	muscle
44	chr15:41002200-41011000	Weak transcription	Fetal Intestine Small	intestine
45	chr15:41002200-41021600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:41002400-41009000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:41002800-41008600	Strong transcription	GM12878-XiMat	blood
48	chr15:41002800-41019400	Weak transcription	Fetal Stomach	stomach
49	chr15:41003200-41007800	Weak transcription	HepG2	liver
50	chr15:41003200-41021800	Weak transcription	Brain Germinal Matrix	brain

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