Variant report

Variant	rs1865260
Chromosome Location	chr2:47207665-47207666
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47204388..47206742-chr2:47207490..47210493,3	K562	blood:
2	chr2:47205588..47209510-chr2:47401817..47405792,7	K562	blood:
3	chr2:47206562..47208636-chr2:47212925..47215220,2	K562	blood:
4	chr2:47205093..47209059-chr2:47402217..47405792,6	K562	blood:

Variant related genes	Relation type
ENSG00000143933	Chromatin interaction
ENSG00000068724	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11893750	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12998344	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13004682	1.00[CEU][hapmap];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13011673	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13025013	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17036004	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17481321	0.86[ASW][hapmap]
rs17540504	0.86[ASW][hapmap]
rs34800049	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs993848	1.00[CEU][hapmap];0.80[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs993849	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv457352	chr2:47004788-47325973	Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
3	nsv581749	chr2:47004788-47325973	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS 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	37 gene(s)	inside rSNPs	diseases
4	nsv1004828	chr2:47056849-47814482	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
5	nsv524970	chr2:47162739-47302095	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
6	nsv1000377	chr2:47189386-47344029	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
7	nsv581750	chr2:47207665-47229953	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1865260	B4GALT5	trans	cerebellum	SCAN
rs1865260	SOCS5	cis	parietal	SCAN
rs1865260	MCFD2	cis	parietal	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47169800-47214600	Weak transcription	Fetal Kidney	kidney
2	chr2:47174400-47212400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr2:47177200-47210400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:47181600-47210800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr2:47185200-47210200	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr2:47185400-47210400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:47187800-47210200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
8	chr2:47195600-47210400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr2:47195600-47212800	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:47196400-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr2:47196600-47227800	Strong transcription	Dnd41	blood
12	chr2:47198000-47209800	Weak transcription	Right Atrium	heart
13	chr2:47198400-47208000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr2:47199200-47208600	Weak transcription	Small Intestine	intestine
15	chr2:47199400-47208400	Weak transcription	HUVEC	blood vessel
16	chr2:47199600-47209600	Strong transcription	Osteobl	bone
17	chr2:47199800-47208400	Strong transcription	Fetal Intestine Small	intestine
18	chr2:47199800-47209600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr2:47200000-47207800	Strong transcription	HepG2	liver
20	chr2:47200000-47207800	Weak transcription	K562	blood
21	chr2:47200200-47208000	Weak transcription	Stomach Mucosa	stomach
22	chr2:47200200-47210000	Weak transcription	Hela-S3	cervix
23	chr2:47200400-47208800	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr2:47200800-47216400	Genic enhancers	Fetal Thymus	thymus
25	chr2:47201400-47209400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr2:47201600-47208600	Strong transcription	A549	lung
27	chr2:47201600-47210200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr2:47201600-47211800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr2:47201600-47213200	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr2:47201800-47208200	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr2:47201800-47208200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr2:47201800-47208400	Strong transcription	Fetal Intestine Large	intestine
33	chr2:47201800-47211600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr2:47202000-47208400	Strong transcription	Fetal Muscle Trunk	muscle
35	chr2:47202000-47208400	Weak transcription	Ovary	ovary
36	chr2:47202000-47209200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr2:47202000-47209400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr2:47202000-47209400	Strong transcription	NHLF	lung
39	chr2:47202000-47211400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr2:47202000-47214800	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr2:47202200-47208000	Strong transcription	Skeletal Muscle Female	skeletal muscle
42	chr2:47202200-47208800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr2:47202200-47208800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:47202200-47209400	Strong transcription	NHDF-Ad	bronchial
45	chr2:47202200-47212600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr2:47202400-47208800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr2:47202600-47208800	Strong transcription	Esophagus	oesophagus
48	chr2:47203400-47208600	Strong transcription	Lung	lung
49	chr2:47203400-47210000	Genic enhancers	Primary B cells from peripheral blood	blood
50	chr2:47203600-47212800	Genic enhancers	Placenta	Placenta

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