Variant report

Variant	rs17557422
Chromosome Location	chr2:47433968-47433969
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:47431418..47435182-chr2:47440517..47443533,3	MCF-7	breast:
2	chr2:47423169..47425083-chr2:47433358..47436246,2	K562	blood:
3	chr2:47433849..47436405-chr2:47465797..47467993,2	MCF-7	breast:
4	chr2:47432369..47434937-chr2:47435735..47438988,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1021609	0.95[ASN][1000 genomes]
rs1021610	0.95[ASN][1000 genomes]
rs1039162	0.81[CHB][hapmap]
rs13391158	0.81[CHB][hapmap]
rs13422681	0.81[ASN][1000 genomes]
rs17485833	0.85[ASW][hapmap]
rs1874668	0.88[ASN][1000 genomes]
rs1874669	0.88[ASN][1000 genomes]
rs2132923	0.85[ASN][1000 genomes]
rs2132924	0.87[ASN][1000 genomes]
rs4952876	0.87[ASN][1000 genomes]
rs4952877	0.81[CHB][hapmap]
rs4953477	0.88[ASN][1000 genomes]
rs4953478	0.88[ASN][1000 genomes]
rs4953479	0.81[CHB][hapmap]
rs61371951	0.93[ASN][1000 genomes]
rs6544972	0.85[ASW][hapmap]
rs6721098	0.88[ASN][1000 genomes]
rs67882902	0.86[ASN][1000 genomes]
rs7575670	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv10649	chr2:47429316-47472670	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv531348	chr2:47433147-47827310	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17557422	CALM2	cis	cerebellum	SCAN
rs17557422	C2orf61	cis	cerebellum	SCAN
rs17557422	CALM2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:47427000-47435200	Weak transcription	Hela-S3	cervix
2	chr2:47427000-47435800	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr2:47428400-47437800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:47428800-47441000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:47428800-47442000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr2:47429000-47438400	Weak transcription	Brain Anterior Caudate	brain
7	chr2:47429200-47435800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr2:47430800-47435800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:47431400-47447200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr2:47431800-47434200	Enhancers	K562	blood
11	chr2:47432200-47435200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr2:47432400-47434400	Enhancers	Placenta	Placenta
13	chr2:47433000-47434000	Enhancers	A549	lung
14	chr2:47433000-47434400	Weak transcription	Lung	lung
15	chr2:47433000-47434800	Weak transcription	Gastric	stomach
16	chr2:47433000-47438400	Weak transcription	Liver	Liver
17	chr2:47433200-47434600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr2:47433200-47435600	Weak transcription	NH-A	brain
19	chr2:47433200-47435800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr2:47433200-47435800	Weak transcription	Fetal Lung	lung
21	chr2:47433200-47435800	Weak transcription	NHLF	lung
22	chr2:47433200-47436000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:47433200-47442200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr2:47433400-47434600	Weak transcription	Spleen	Spleen
25	chr2:47433400-47435800	Weak transcription	Fetal Intestine Small	intestine
26	chr2:47433400-47435800	Weak transcription	Osteobl	bone
27	chr2:47433400-47436000	Weak transcription	HSMM	muscle
28	chr2:47433400-47442200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr2:47433400-47445200	Weak transcription	Fetal Kidney	kidney
30	chr2:47433600-47435800	Weak transcription	Stomach Mucosa	stomach
31	chr2:47433600-47435800	Weak transcription	HUVEC	blood vessel
32	chr2:47433600-47438400	Weak transcription	Fetal Heart	heart
33	chr2:47433800-47435000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr2:47433800-47435800	Weak transcription	Fetal Intestine Large	intestine
35	chr2:47433800-47436000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links