Variant report

Variant	rs2682582
Chromosome Location	chr19:43966929-43966930
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:43965066..43971111-chr19:44006791..44009897,14	MCF-7	breast:
2	chr19:43964006..43968075-chr19:43982623..43986349,3	MCF-7	breast:
3	chr19:43966525..43969059-chr19:44008556..44010178,2	K562	blood:
4	chr19:43966113..43971089-chr19:44005040..44010546,6	K562	blood:

Variant related genes	Relation type
ENSG00000176531	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11668793	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2260164	1.00[CEU][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599433	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599434	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599437	0.81[CEU][hapmap]
rs2599438	1.00[CEU][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599441	0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2599442	1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[ASN][1000 genomes]
rs2682568	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2682583	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35107209	0.91[ASN][1000 genomes]
rs57029828	0.89[ASN][1000 genomes]
rs60027199	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1055872	chr19:43173614-44075193	Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
2	nsv544009	chr19:43173614-44075193	Enhancers ZNF genes & repeats Genic enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv1067126	chr19:43260649-44075194	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	nsv544015	chr19:43260649-44075194	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
5	nsv1057657	chr19:43302497-44076564	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
6	nsv1059631	chr19:43316978-44075054	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
7	nsv544030	chr19:43316978-44075054	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
8	nsv532820	chr19:43807486-44080610	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
9	nsv1056721	chr19:43808474-44095077	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv532821	chr19:43842383-44357315	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
11	nsv1058162	chr19:43846238-44055058	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
12	nsv2501	chr19:43942581-43978424	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2682582	BCAT2	cis	cerebellum	SCAN
rs2682582	SEC1	cis	cerebellum	SCAN
rs2682582	SIGLEC14	cis	parietal	SCAN
rs2682582	NANOS2	cis	parietal	SCAN
rs2682582	SLC8A2	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:43957000-43967000	Weak transcription	Spleen	Spleen
2	chr19:43959800-43967000	Weak transcription	Colon Smooth Muscle	Colon
3	chr19:43960200-43967000	Weak transcription	Colonic Mucosa	Colon
4	chr19:43960200-43967000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr19:43960200-43967000	Weak transcription	Placenta	Placenta
6	chr19:43960200-43967400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr19:43960400-43967000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr19:43960400-43967000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr19:43960400-43967000	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr19:43960600-43967000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr19:43964000-43967200	Weak transcription	Ovary	ovary
12	chr19:43964600-43967000	Enhancers	HepG2	liver
13	chr19:43964800-43967000	Strong transcription	NHEK	skin
14	chr19:43966200-43967000	Enhancers	Primary T cells from cord blood	blood
15	chr19:43966200-43967000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr19:43966400-43967000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr19:43966400-43967000	Enhancers	Primary T helper naive cells from peripheral blood	blood
18	chr19:43966400-43967000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
19	chr19:43966400-43967000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr19:43966400-43967000	Genic enhancers	Esophagus	oesophagus
21	chr19:43966400-43967400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr19:43966600-43967000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr19:43966600-43967000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr19:43966600-43967000	Enhancers	Placenta Amnion	Placenta Amnion
25	chr19:43966600-43967000	Enhancers	Thymus	Thymus
26	chr19:43966600-43967200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
27	chr19:43966600-43967400	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
28	chr19:43966600-43968600	Active TSS	H9 Cell Line	embryonic stem cell
29	chr19:43966600-43968600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr19:43966800-43967000	Flanking Active TSS	H1 Cell Line	embryonic stem cell
31	chr19:43966800-43967000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr19:43966800-43967000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:43966800-43967000	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
34	chr19:43966800-43967000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:43966800-43967000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
36	chr19:43966800-43967000	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr19:43966800-43967000	Enhancers	Adipose Nuclei	Adipose
38	chr19:43966800-43967000	Enhancers	Rectal Mucosa Donor 31	rectum
39	chr19:43966800-43967200	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:43966800-43967200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
41	chr19:43966800-43967200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
42	chr19:43966800-43967200	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr19:43966800-43967400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
44	chr19:43966800-43967400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr19:43966800-43967400	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr19:43966800-43967400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr19:43966800-43967800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
48	chr19:43966800-43968200	Active TSS	Stomach Smooth Muscle	stomach
49	chr19:43966800-43968600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
50	chr19:43966800-43968600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell

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