Variant report

Variant	rs1706808
Chromosome Location	chr15:45451233-45451234
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:45449920..45453086-chr15:45456416..45459415,4	K562	blood:
2	chr15:45443966..45446125-chr15:45449579..45451751,2	K562	blood:
3	chr15:45449609..45453236-chr15:45457803..45460650,4	K562	blood:

Variant related genes	Relation type
ENSG00000259539	Chromatin interaction
ENSG00000137857	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1620253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648304	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648310	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648312	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648313	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1648318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706807	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706811	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706812	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706815	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1706817	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706826	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706827	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1706829	1.00[JPT][hapmap]
rs2162246	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2292468	1.00[CEU][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes]
rs2458237	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467819	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2467820	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6493143	1.00[JPT][hapmap]
rs7169193	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv427961	chr15:45338381-45491634	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
4	nsv457124	chr15:45381998-45460422	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
5	nsv569312	chr15:45381998-45460422	Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
6	esv1823029	chr15:45387102-45482245	Bivalent Enhancer Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
7	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
8	nsv569313	chr15:45413541-45457458	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv518213	chr15:45421758-45464768	Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv520580	chr15:45438537-45457349	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
11	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
12	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1706808	GATM	cis	lymphoblastoid	seeQTL
rs1706808	CCNDBP1	cis	cerebellum	SCAN
rs1706808	FSIP1	cis	parietal	SCAN
rs1706808	SHF	cis	parietal	SCAN
rs1706808	SHF	cis	cerebellum	SCAN
rs1706808	ADAL	cis	parietal	SCAN

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45427600-45458600	Weak transcription	Right Atrium	heart
2	chr15:45434800-45457800	Weak transcription	Adipose Nuclei	Adipose
3	chr15:45438800-45455000	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr15:45439000-45454800	Weak transcription	Stomach Mucosa	stomach
5	chr15:45439000-45457800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:45439000-45458000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr15:45439400-45454800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr15:45439800-45455000	Weak transcription	Skeletal Muscle Male	skeletal muscle
9	chr15:45440400-45455000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr15:45440400-45458600	Weak transcription	Aorta	Aorta
11	chr15:45441000-45458000	Weak transcription	Primary T cells from cord blood	blood
12	chr15:45441200-45458000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr15:45441600-45454800	Weak transcription	Left Ventricle	heart
14	chr15:45441800-45454200	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr15:45442000-45455000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr15:45442200-45455000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
17	chr15:45442200-45457600	Weak transcription	Small Intestine	intestine
18	chr15:45442400-45458000	Weak transcription	Primary B cells from cord blood	blood
19	chr15:45443400-45458000	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:45444600-45453800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:45444600-45455000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr15:45444800-45454800	Weak transcription	Pancreas	Pancrea
23	chr15:45444800-45454800	Weak transcription	Spleen	Spleen
24	chr15:45444800-45455200	Weak transcription	Ovary	ovary
25	chr15:45444800-45457400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:45445000-45454800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:45445000-45455000	Weak transcription	Fetal Intestine Large	intestine
28	chr15:45445000-45455000	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:45445000-45455000	Weak transcription	Fetal Stomach	stomach
30	chr15:45445000-45455000	Weak transcription	Thymus	Thymus
31	chr15:45445200-45455200	Weak transcription	Right Ventricle	heart
32	chr15:45448400-45457800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr15:45449000-45451400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr15:45449000-45451400	Enhancers	Cortex derived primary cultured neurospheres	brain
35	chr15:45449000-45451400	Enhancers	Brain Hippocampus Middle	brain
36	chr15:45449000-45451400	Enhancers	Brain Substantia Nigra	brain
37	chr15:45449000-45451400	Enhancers	Placenta	Placenta
38	chr15:45449400-45452600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr15:45449400-45455000	Weak transcription	Fetal Muscle Trunk	muscle
40	chr15:45449400-45457200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:45449400-45458600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:45449800-45455000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:45450200-45451400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:45450200-45454800	Weak transcription	HSMM	muscle
45	chr15:45450400-45452400	Weak transcription	Gastric	stomach
46	chr15:45450400-45453800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr15:45450400-45454800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr15:45450400-45454800	Weak transcription	Fetal Intestine Small	intestine
49	chr15:45450400-45455200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr15:45450400-45455200	Weak transcription	K562	blood

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