Variant report

Variant	rs2253519
Chromosome Location	chr2:38809162-38809163
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38808368..38809303-chr2:38952790..38953819,4	K562	blood:
2	chr2:38807538..38810280-chr2:38962388..38964852,2	K562	blood:
3	chr2:38806174..38811270-chr2:38966687..38973672,10	K562	blood:
4	chr2:38805174..38810149-chr2:38974397..38979817,14	K562	blood:
5	chr2:38807225..38809516-chr2:38810763..38812911,2	MCF-7	breast:
6	chr2:38794380..38796930-chr2:38807297..38810319,3	MCF-7	breast:
7	chr2:38802059..38810352-chr2:38974835..38979723,14	K562	blood:
8	chr2:38807567..38810136-chr2:38951744..38953285,2	MCF-7	breast:
9	chr2:38807837..38810352-chr2:38947655..38950217,2	K562	blood:
10	chr2:38807176..38809738-chr2:38829529..38831599,2	MCF-7	breast:
11	chr2:38808750..38809492-chr2:38952829..38953803,4	MCF-7	breast:
12	chr2:38808219..38810400-chr2:38813062..38815014,2	MCF-7	breast:
13	chr2:38806614..38812442-chr2:38966843..38970976,5	K562	blood:
14	chr2:38801102..38805914-chr2:38807147..38811065,7	MCF-7	breast:
15	chr2:38805850..38810073-chr2:38814750..38818900,5	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000143889	Chromatin interaction
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10495880	0.82[EUR][1000 genomes]
rs12329205	0.81[CEU][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12622497	0.84[JPT][hapmap]
rs12712608	0.83[ASN][1000 genomes]
rs12987111	0.83[EUR][1000 genomes]
rs12990659	0.83[EUR][1000 genomes]
rs12995222	0.82[EUR][1000 genomes]
rs12996029	0.82[EUR][1000 genomes]
rs13431551	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1368114	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1540436	0.82[EUR][1000 genomes]
rs1579537	1.00[CEU][hapmap];0.87[JPT][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17022904	0.94[JPT][hapmap];0.88[ASN][1000 genomes]
rs17022996	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs17023003	0.87[CHD][hapmap]
rs17493573	0.83[EUR][1000 genomes]
rs2116385	0.83[JPT][hapmap]
rs2373421	0.90[CEU][hapmap];0.83[JPT][hapmap]
rs2373423	0.81[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs34462852	0.82[EUR][1000 genomes]
rs35219064	0.81[EUR][1000 genomes]
rs35734673	0.82[EUR][1000 genomes]
rs36057155	0.90[EUR][1000 genomes]
rs4268910	0.83[EUR][1000 genomes]
rs6544169	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6721860	0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.82[LWK][hapmap];0.89[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6727476	0.88[ASN][1000 genomes]
rs6733950	0.87[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs6736320	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6742843	0.83[JPT][hapmap]
rs6745646	0.89[CEU][hapmap]
rs6749343	0.84[EUR][1000 genomes]
rs6757844	0.81[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs67772386	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs72907903	0.82[EUR][1000 genomes]
rs7571463	0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap]
rs7609065	0.83[AMR][1000 genomes];0.90[EUR][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	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581482	chr2:38799820-38858669	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2253519	CRIM1	cis	parietal	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38763600-38809600	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr2:38768200-38812800	Weak transcription	Psoas Muscle	Psoas
3	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
6	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
7	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
8	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
9	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
12	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr2:38792600-38810200	Strong transcription	K562	blood
15	chr2:38795200-38809200	Weak transcription	Fetal Intestine Small	intestine
16	chr2:38795200-38809200	Weak transcription	Fetal Stomach	stomach
17	chr2:38795200-38814800	Weak transcription	Gastric	stomach
18	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
19	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach
20	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
21	chr2:38798200-38812800	Weak transcription	Fetal Muscle Leg	muscle
22	chr2:38798200-38812800	Weak transcription	Thymus	Thymus
23	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr2:38798600-38816400	Weak transcription	Brain Germinal Matrix	brain
27	chr2:38798800-38817000	Weak transcription	Brain Anterior Caudate	brain
28	chr2:38798800-38822000	Weak transcription	NHEK	skin
29	chr2:38799600-38817200	Weak transcription	Brain Substantia Nigra	brain
30	chr2:38799800-38827800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:38800000-38814000	Strong transcription	HSMM	muscle
32	chr2:38800000-38817800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr2:38800000-38818600	Strong transcription	Monocytes-CD14+_RO01746	blood
34	chr2:38800600-38816600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr2:38802800-38819000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
36	chr2:38803600-38813000	Strong transcription	Duodenum Mucosa	Duodenum
37	chr2:38803600-38813200	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr2:38805200-38811800	Weak transcription	Fetal Brain Male	brain
39	chr2:38805200-38826400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr2:38806200-38809200	Genic enhancers	HUES64 Cell Line	embryonic stem cell
41	chr2:38806400-38814200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
42	chr2:38806800-38813000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr2:38807000-38809200	Genic enhancers	HUES48 Cell Line	embryonic stem cell
44	chr2:38807000-38809200	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:38807000-38809200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr2:38807000-38809400	Genic enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr2:38807000-38809400	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
48	chr2:38807200-38809200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:38807200-38809200	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr2:38807200-38809400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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