Variant report

Variant	rs13431551
Chromosome Location	chr2:38805596-38805597
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:38803779..38806486-chr2:38953077..38954678,2	MCF-7	breast:
2	chr2:38805174..38810149-chr2:38974397..38979817,14	K562	blood:
3	chr2:38801102..38805914-chr2:38807147..38811065,7	MCF-7	breast:
4	chr2:38802059..38810352-chr2:38974835..38979723,14	K562	blood:
5	chr2:38788831..38791185-chr2:38805225..38808104,2	K562	blood:
6	chr2:38805084..38807176-chr2:38944983..38947545,2	K562	blood:
7	chr2:38800010..38801943-chr2:38804544..38806544,2	MCF-7	breast:
8	chr2:38805216..38808046-chr2:38947623..38949999,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10495880	0.83[EUR][1000 genomes]
rs12105070	0.80[ASN][1000 genomes]
rs12329205	0.81[CEU][hapmap];0.87[CHB][hapmap];0.93[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs12622497	0.84[JPT][hapmap]
rs12712608	0.84[ASN][1000 genomes]
rs12987111	0.81[EUR][1000 genomes]
rs12990659	0.81[EUR][1000 genomes]
rs12991911	0.80[EUR][1000 genomes]
rs12995222	0.83[EUR][1000 genomes]
rs12996029	0.83[EUR][1000 genomes]
rs1368114	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1540436	0.80[EUR][1000 genomes]
rs1579537	1.00[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17022904	0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs17022996	0.90[CEU][hapmap];0.83[JPT][hapmap];0.82[YRI][hapmap];0.81[AMR][1000 genomes]
rs17023003	0.87[CHD][hapmap];0.82[MKK][hapmap];0.83[YRI][hapmap]
rs17493573	0.81[EUR][1000 genomes]
rs2116385	0.83[JPT][hapmap]
rs2253519	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]
rs2373421	0.90[CEU][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs2373423	0.89[ASW][hapmap];0.81[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[YRI][hapmap];0.94[ASN][1000 genomes]
rs34450185	0.81[AFR][1000 genomes]
rs34462852	0.83[EUR][1000 genomes]
rs35219064	0.82[EUR][1000 genomes]
rs35734673	0.83[EUR][1000 genomes]
rs36057155	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3731841	0.80[ASN][1000 genomes]
rs4268910	0.81[EUR][1000 genomes]
rs6544169	1.00[CEU][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6721860	0.93[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.89[TSI][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6727476	0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs6733950	0.87[CHD][hapmap];0.92[GIH][hapmap];0.81[TSI][hapmap]
rs6736320	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6742843	0.83[JPT][hapmap]
rs6745646	0.89[CEU][hapmap];0.95[YRI][hapmap]
rs6749343	0.85[EUR][1000 genomes]
rs6757844	1.00[ASW][hapmap];0.81[CEU][hapmap];0.87[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.85[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs67772386	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72907903	0.83[EUR][1000 genomes]
rs7571463	0.90[CHD][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.85[TSI][hapmap]
rs7609065	0.94[AMR][1000 genomes];0.91[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
rs13431551	CRIM1	cis	parietal	SCAN

Chromatin state (count:120 , 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	chr2:38777000-38807200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr2:38779000-38818200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr2:38779400-38821800	Weak transcription	Right Ventricle	heart
7	chr2:38779600-38807400	Weak transcription	Fetal Heart	heart
8	chr2:38779600-38812800	Weak transcription	Aorta	Aorta
9	chr2:38781200-38827600	Weak transcription	Esophagus	oesophagus
10	chr2:38782400-38819000	Strong transcription	Fetal Thymus	thymus
11	chr2:38783800-38827800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr2:38785000-38827600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr2:38786000-38827600	Weak transcription	Colonic Mucosa	Colon
14	chr2:38786400-38806200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr2:38786400-38818800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr2:38786600-38819000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr2:38787200-38805600	Strong transcription	HUES6 Cell Line	embryonic stem cell
18	chr2:38787200-38806200	Strong transcription	HUES64 Cell Line	embryonic stem cell
19	chr2:38787200-38807000	Strong transcription	HUES48 Cell Line	embryonic stem cell
20	chr2:38787200-38807000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr2:38787400-38806400	Strong transcription	Dnd41	blood
22	chr2:38790800-38807000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr2:38792600-38810200	Strong transcription	K562	blood
24	chr2:38795200-38807200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr2:38795200-38808400	Weak transcription	Left Ventricle	heart
26	chr2:38795200-38808400	Weak transcription	Lung	lung
27	chr2:38795200-38808400	Weak transcription	Ovary	ovary
28	chr2:38795200-38809200	Weak transcription	Fetal Intestine Small	intestine
29	chr2:38795200-38809200	Weak transcription	Fetal Stomach	stomach
30	chr2:38795200-38814800	Weak transcription	Gastric	stomach
31	chr2:38795400-38808200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
32	chr2:38795600-38808400	Weak transcription	Brain Cingulate Gyrus	brain
33	chr2:38796200-38808200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr2:38796400-38808400	Weak transcription	Brain Angular Gyrus	brain
35	chr2:38796400-38812800	Weak transcription	Small Intestine	intestine
36	chr2:38796600-38808600	Weak transcription	Brain Hippocampus Middle	brain
37	chr2:38797000-38806000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
38	chr2:38798000-38808000	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:38798000-38818000	Weak transcription	Stomach Mucosa	stomach
40	chr2:38798000-38827600	Weak transcription	Spleen	Spleen
41	chr2:38798200-38808000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr2:38798200-38808400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:38798200-38808400	Weak transcription	Pancreas	Pancrea
44	chr2:38798200-38812800	Weak transcription	Fetal Muscle Leg	muscle
45	chr2:38798200-38812800	Weak transcription	Thymus	Thymus
46	chr2:38798200-38820600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr2:38798200-38821800	Weak transcription	Sigmoid Colon	Sigmoid Colon
48	chr2:38798200-38827600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr2:38798400-38806000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr2:38798600-38808000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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