Variant report

Variant	rs815816
Chromosome Location	chr2:47398394-47398395
allele	C/T
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:47183155..47186488-chr2:47397465..47400256,3	K562	blood:
2	chr2:47229922..47232405-chr2:47395571..47398538,2	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	chr2:47396770..47398576-chr2:47595818..47597793,2	MCF-7	breast:
8	chr2:47396296..47398921-chr2:47474804..47476304,2	MCF-7	breast:
9	chr2:47398263..47400819-chr2:47535902..47539310,3	MCF-7	breast:
10	chr2:47217582..47220459-chr2:47397883..47399743,2	MCF-7	breast:
11	chr2:47267673..47270387-chr2:47397211..47399730,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000119888	Chromatin interaction
ENSG00000068724	Chromatin interaction
ENSG00000272814	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11125126	0.90[CHB][hapmap];0.90[CHD][hapmap];0.80[ASN][1000 genomes]
rs12991318	0.90[CHB][hapmap]
rs13390912	0.80[EUR][1000 genomes]
rs13430277	0.80[CHB][hapmap]
rs1630239	0.81[ASN][1000 genomes]
rs1693863	0.81[ASN][1000 genomes]
rs1693864	0.86[ASN][1000 genomes]
rs1693869	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1693882	0.91[ASN][1000 genomes]
rs1723482	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1723483	0.95[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1723484	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1723493	0.92[CEU][hapmap];0.93[MEX][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1995108	0.81[ASN][1000 genomes]
rs2454081	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2454082	0.90[ASN][1000 genomes]
rs2454083	0.90[ASN][1000 genomes]
rs6713934	0.81[ASN][1000 genomes]
rs6751198	0.80[ASN][1000 genomes]
rs7596698	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7606478	0.81[ASN][1000 genomes]
rs815802	1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs815807	0.92[CEU][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs815815	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	0.80[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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs815816	CALM2	cis	cerebellum	SCAN
rs815816	C2orf61	cis	cerebellum	SCAN
rs815816	CALM2	cis	parietal	SCAN
rs815816	TTC7A	cis	cerebellum	SCAN
rs815816	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	chr2:47385400-47398400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
5	chr2:47385400-47398600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr2:47385400-47398800	Strong transcription	Primary hematopoietic stem cells short term culture	blood
7	chr2:47385600-47398600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
8	chr2:47386000-47398800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:47386600-47399000	Genic enhancers	HepG2	liver
10	chr2:47387600-47401400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:47387600-47402200	Weak transcription	Gastric	stomach
12	chr2:47387800-47402000	Weak transcription	Pancreas	Pancrea
13	chr2:47389200-47402000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr2:47389400-47400200	Weak transcription	Colonic Mucosa	Colon
15	chr2:47390000-47402000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr2:47390200-47399200	Weak transcription	Fetal Kidney	kidney
17	chr2:47391000-47398800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:47391800-47400000	Weak transcription	Spleen	Spleen
19	chr2:47392400-47399400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr2:47393200-47398600	Weak transcription	Primary hematopoietic stem cells	blood
21	chr2:47394800-47402000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:47395600-47399200	Genic enhancers	HSMM	muscle
23	chr2:47396200-47398600	Genic enhancers	Osteobl	bone
24	chr2:47396200-47399400	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr2:47396200-47399600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
26	chr2:47396400-47399600	Enhancers	Stomach Mucosa	stomach
27	chr2:47396400-47400800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr2:47396600-47399200	Weak transcription	Fetal Muscle Leg	muscle
29	chr2:47396600-47399400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr2:47396600-47399800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr2:47396600-47400000	Weak transcription	Fetal Stomach	stomach
32	chr2:47396800-47398800	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr2:47396800-47399200	Genic enhancers	Adipose Nuclei	Adipose
34	chr2:47396800-47399200	Enhancers	Fetal Intestine Small	intestine
35	chr2:47396800-47399400	Genic enhancers	Duodenum Mucosa	Duodenum
36	chr2:47396800-47400600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr2:47396800-47401200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr2:47396800-47401200	Transcr. at gene 5' and 3'	A549	lung
39	chr2:47396800-47401200	Transcr. at gene 5' and 3'	NHLF	lung
40	chr2:47396800-47402000	Enhancers	Small Intestine	intestine
41	chr2:47396800-47402600	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr2:47397000-47398600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr2:47397000-47399400	Weak transcription	Right Ventricle	heart
44	chr2:47397000-47400200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr2:47397000-47401000	Enhancers	Liver	Liver
46	chr2:47397000-47401400	Transcr. at gene 5' and 3'	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:47397000-47402000	Weak transcription	Lung	lung
48	chr2:47397200-47398400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr2:47397200-47398600	Transcr. at gene 5' and 3'	NH-A	brain
50	chr2:47397200-47399000	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach

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