Variant report

Variant	rs17493370
Chromosome Location	chr2:38780274-38780275
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:38773369..38778839-chr2:38780028..38785171,8	K562	blood:
2	chr2:38779577..38781346-chr2:38785397..38787246,2	K562	blood:
3	chr2:38768041..38770034-chr2:38779562..38781817,2	K562	blood:
4	chr2:38601876..38603908-chr2:38779549..38781640,2	K562	blood:
5	chr2:38780198..38783785-chr2:38971693..38974497,3	K562	blood:
6	chr2:38778308..38782276-chr2:38966801..38969709,4	K562	blood:

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000119787	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10204680	0.83[CHD][hapmap];0.91[MEX][hapmap]
rs10495880	0.86[CEU][hapmap];0.95[CHD][hapmap];1.00[MEX][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12105827	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12987111	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12990659	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12991911	0.86[CEU][hapmap]
rs12995222	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12996029	0.89[ASW][hapmap];0.80[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.81[TSI][hapmap];0.81[YRI][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1540436	1.00[JPT][hapmap];0.85[YRI][hapmap];0.84[ASN][1000 genomes]
rs17421378	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17421399	1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17421503	0.89[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17421545	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17421587	0.97[EUR][1000 genomes]
rs17421743	0.80[CEU][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs17493321	1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs17493363	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17493419	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17493538	1.00[ASW][hapmap];0.91[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes]
rs17493573	0.86[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17575960	0.86[CEU][hapmap];0.94[EUR][1000 genomes]
rs17603796	1.00[CHB][hapmap];0.90[JPT][hapmap];0.97[ASN][1000 genomes]
rs1864828	0.90[JPT][hapmap]
rs1864829	0.84[ASN][1000 genomes]
rs1864830	0.84[ASN][1000 genomes]
rs34218951	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs34462852	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35734673	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3731843	0.82[JPT][hapmap]
rs4268910	0.89[ASW][hapmap];0.80[CEU][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.83[LWK][hapmap];0.85[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6544170	0.91[CHD][hapmap];1.00[GIH][hapmap];0.91[MEX][hapmap]
rs6733848	0.85[CHD][hapmap]
rs68109027	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72795154	1.00[EUR][1000 genomes]
rs72905846	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs72905865	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72907903	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7573095	0.82[AFR][1000 genomes]
rs7574556	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs919698	0.80[CEU][hapmap];0.94[EUR][1000 genomes]
rs934394	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs934395	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[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	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	esv1796304	chr2:38766721-38790750	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17493370	CRIM1	cis	parietal	SCAN

Chromatin state (count:94 , 50 per page) page: 1 2

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	chr2:38768400-38787800	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr2:38768400-38788000	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:38768400-38791600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr2:38769000-38793200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr2:38769200-38782800	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:38769200-38787800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:38769200-38788400	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr2:38770000-38788600	Weak transcription	Colon Smooth Muscle	Colon
11	chr2:38770200-38781000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:38770400-38786600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr2:38770400-38787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr2:38770400-38787200	Weak transcription	Duodenum Mucosa	Duodenum
15	chr2:38770400-38787200	Weak transcription	Fetal Intestine Large	intestine
16	chr2:38770400-38787200	Weak transcription	NHLF	lung
17	chr2:38770400-38787200	Weak transcription	Osteobl	bone
18	chr2:38770400-38787400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr2:38770400-38787400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr2:38770400-38791000	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr2:38770400-38794600	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr2:38770600-38785800	Weak transcription	NH-A	brain
23	chr2:38770600-38787400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr2:38770600-38794800	Weak transcription	NHEK	skin
25	chr2:38770800-38794400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:38771000-38786200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr2:38771200-38781000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr2:38771200-38787200	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr2:38771200-38787400	Weak transcription	HUVEC	blood vessel
30	chr2:38772800-38787400	Weak transcription	HepG2	liver
31	chr2:38775200-38783600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:38775600-38781200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr2:38775800-38821800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr2:38776400-38787400	Weak transcription	Fetal Kidney	kidney
35	chr2:38776600-38787200	Weak transcription	Brain Inferior Temporal Lobe	brain
36	chr2:38776600-38787400	Weak transcription	Placenta	Placenta
37	chr2:38776600-38788000	Weak transcription	Brain Germinal Matrix	brain
38	chr2:38776600-38791000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr2:38776800-38782000	Weak transcription	Fetal Brain Female	brain
40	chr2:38776800-38785200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr2:38776800-38787200	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr2:38776800-38787200	Weak transcription	Fetal Lung	lung
43	chr2:38776800-38787400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr2:38776800-38788800	Weak transcription	Fetal Brain Male	brain
45	chr2:38777000-38787200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
46	chr2:38777000-38794600	Weak transcription	Brain Anterior Caudate	brain
47	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr2:38777200-38787200	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr2:38777200-38794200	Weak transcription	Ovary	ovary
50	chr2:38777400-38781000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links