Variant report

Variant	rs815815
Chromosome Location	chr2:47399064-47399065
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47398506..47400133-chr2:47537850..47540802,2	K562	blood:
2	chr2:47183155..47186488-chr2:47397465..47400256,3	K562	blood:
3	chr2:47301037..47304852-chr2:47397378..47400468,3	MCF-7	breast:
4	chr2:47252232..47263251-chr2:47397787..47406051,20	MCF-7	breast:
5	chr2:47397654..47400175-chr2:47508380..47511967,3	K562	blood:
6	chr2:47241103..47242640-chr2:47398304..47400059,2	MCF-7	breast:
7	chr2:47398263..47400819-chr2:47535902..47539310,3	MCF-7	breast:
8	chr2:47217582..47220459-chr2:47397883..47399743,2	MCF-7	breast:
9	chr2:47267673..47270387-chr2:47397211..47399730,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000068724	Chromatin interaction
ENSG00000272814	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11125126	0.90[CHB][hapmap];0.90[CHD][hapmap];0.87[ASN][1000 genomes]
rs12991318	0.90[CHB][hapmap]
rs13390912	0.81[EUR][1000 genomes]
rs13430277	0.81[CEU][hapmap];0.80[CHB][hapmap]
rs1404770	0.83[ASN][1000 genomes]
rs1630239	0.88[ASN][1000 genomes]
rs1693863	0.88[ASN][1000 genomes]
rs1693864	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1693869	0.92[CEU][hapmap];0.82[JPT][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1693882	0.95[ASN][1000 genomes]
rs1723482	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1723483	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1723484	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1723493	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[MEX][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1995108	0.86[ASN][1000 genomes]
rs2454081	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2454082	0.98[ASN][1000 genomes]
rs2454083	0.98[ASN][1000 genomes]
rs2462588	0.86[ASN][1000 genomes]
rs2462589	0.86[ASN][1000 genomes]
rs6713934	0.88[ASN][1000 genomes]
rs6751198	0.87[ASN][1000 genomes]
rs72879030	0.81[ASN][1000 genomes]
rs7596698	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7606478	0.88[ASN][1000 genomes]
rs815802	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs815807	1.00[CEU][hapmap];0.87[GIH][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap];0.84[EUR][1000 genomes]
rs815816	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs815817	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	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
3	nsv457374	chr2:47313624-47448865	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Active TSS Bivalent Enhancer 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	87 gene(s)	inside rSNPs	diseases
4	nsv581754	chr2:47313624-47448865	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Dialysis-related mortality	21546767	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs815815	CALM2	cis	cerebellum	SCAN
rs815815	TTC7A	cis	cerebellum	SCAN
rs815815	CALM2	cis	parietal	SCAN
rs815815	C2orf61	cis	cerebellum	SCAN
rs815815	THADA	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47366800-47399400	Strong transcription	Fetal Thymus	thymus
2	chr2:47367000-47401200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:47367200-47402000	Weak transcription	Esophagus	oesophagus
4	chr2:47387600-47401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:47387600-47402200	Weak transcription	Gastric	stomach
6	chr2:47387800-47402000	Weak transcription	Pancreas	Pancrea
7	chr2:47389200-47402000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:47389400-47400200	Weak transcription	Colonic Mucosa	Colon
9	chr2:47390000-47402000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr2:47390200-47399200	Weak transcription	Fetal Kidney	kidney
11	chr2:47391800-47400000	Weak transcription	Spleen	Spleen
12	chr2:47392400-47399400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr2:47394800-47402000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr2:47395600-47399200	Genic enhancers	HSMM	muscle
15	chr2:47396200-47399400	Enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:47396200-47399600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:47396400-47399600	Enhancers	Stomach Mucosa	stomach
18	chr2:47396400-47400800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
19	chr2:47396600-47399200	Weak transcription	Fetal Muscle Leg	muscle
20	chr2:47396600-47399400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr2:47396600-47399800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr2:47396600-47400000	Weak transcription	Fetal Stomach	stomach
23	chr2:47396800-47399200	Genic enhancers	Adipose Nuclei	Adipose
24	chr2:47396800-47399200	Enhancers	Fetal Intestine Small	intestine
25	chr2:47396800-47399400	Genic enhancers	Duodenum Mucosa	Duodenum
26	chr2:47396800-47400600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr2:47396800-47401200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr2:47396800-47401200	Transcr. at gene 5' and 3'	A549	lung
29	chr2:47396800-47401200	Transcr. at gene 5' and 3'	NHLF	lung
30	chr2:47396800-47402000	Enhancers	Small Intestine	intestine
31	chr2:47396800-47402600	Transcr. at gene 5' and 3'	Dnd41	blood
32	chr2:47397000-47399400	Weak transcription	Right Ventricle	heart
33	chr2:47397000-47400200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr2:47397000-47401000	Enhancers	Liver	Liver
35	chr2:47397000-47401400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr2:47397000-47402000	Weak transcription	Lung	lung
37	chr2:47397200-47399200	Genic enhancers	NHEK	skin
38	chr2:47397200-47399400	Genic enhancers	HUVEC	blood vessel
39	chr2:47397400-47399200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
40	chr2:47397400-47399200	Genic enhancers	Rectal Mucosa Donor 29	rectum
41	chr2:47397400-47400200	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:47397400-47400600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr2:47397600-47399400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:47397600-47399400	Enhancers	Ovary	ovary
45	chr2:47397600-47400000	Genic enhancers	HUES48 Cell Line	embryonic stem cell
46	chr2:47397600-47400400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr2:47397600-47400400	Enhancers	Fetal Lung	lung
48	chr2:47397600-47401800	Weak transcription	Placenta	Placenta
49	chr2:47397800-47399200	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:47397800-47399200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin

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