Variant report

Variant	rs13017968
Chromosome Location	chr2:40574672-40574673
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:40569259..40571407-chr2:40573018..40575519,2	K562	blood:

Extended variants
information (count: 69 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10165478	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10168748	0.85[CHB][hapmap]
rs10171704	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs10177941	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs10178405	0.81[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10181007	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10189274	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10192458	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10192546	0.81[CHB][hapmap]
rs10490051	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11690171	0.81[CHB][hapmap]
rs11691852	0.84[ASN][1000 genomes]
rs12471797	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12613022	0.98[ASN][1000 genomes]
rs12987979	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs12988856	0.81[CHB][hapmap]
rs12989200	0.85[CHB][hapmap]
rs12989852	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs12995004	0.81[CHB][hapmap]
rs12996962	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13014950	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs13022231	0.95[CEU][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13031340	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13031441	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13032770	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13405065	0.81[CHB][hapmap]
rs1477002	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1477004	0.81[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs1477005	0.84[ASN][1000 genomes]
rs1861293	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2192776	0.88[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2192779	1.00[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2373857	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs2373859	0.81[CHB][hapmap];0.81[CHD][hapmap];0.84[JPT][hapmap];0.91[MEX][hapmap]
rs2888676	0.90[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4446101	0.90[CHB][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4452199	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4452200	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4552227	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4588235	0.90[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4645043	0.81[CEU][hapmap];0.95[CHB][hapmap];0.81[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4952409	0.90[CHB][hapmap];0.90[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs6544323	0.81[CHB][hapmap]
rs6544324	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs6544330	0.86[CHB][hapmap];0.83[MEX][hapmap]
rs6544333	0.89[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs6544334	0.86[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap];0.82[JPT][hapmap];0.86[ASN][1000 genomes]
rs6718322	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6738580	0.86[CHB][hapmap]
rs6738673	0.81[CHB][hapmap]
rs6747285	0.83[ASN][1000 genomes]
rs7424049	0.90[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs7598561	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7599953	0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs918002	0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9309055	0.84[ASN][1000 genomes]
rs967351	0.81[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.90[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs981739	0.95[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs984707	1.00[CHB][hapmap];0.92[CHD][hapmap];0.82[GIH][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs990270	0.81[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv34071	chr2:40435231-40578229	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1010508	chr2:40526981-40590777	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv535655	chr2:40526981-40590777	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv873914	chr2:40573350-40586022	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13017968	CRIM1	cis	cerebellum	SCAN
rs13017968	EML4	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40543200-40578800	Weak transcription	Primary monocytes fromperipheralblood	blood
2	chr2:40552800-40590600	Weak transcription	Fetal Kidney	kidney
3	chr2:40560200-40579000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr2:40566200-40575600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr2:40568600-40575800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr2:40570200-40575600	Enhancers	Muscle Satellite Cultured Cells	--
7	chr2:40570400-40576800	Enhancers	NHDF-Ad	bronchial
8	chr2:40571000-40577000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr2:40571400-40576000	Enhancers	Right Atrium	heart
10	chr2:40571400-40576800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr2:40571600-40575600	Weak transcription	HMEC	breast
12	chr2:40571600-40582600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:40573200-40574800	Enhancers	Dnd41	blood
14	chr2:40573200-40577000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr2:40573400-40576800	Enhancers	NHLF	lung
16	chr2:40573400-40577200	Enhancers	HSMM	muscle
17	chr2:40573600-40576800	Enhancers	NH-A	brain
18	chr2:40574000-40579600	Weak transcription	Colon Smooth Muscle	Colon
19	chr2:40574200-40574800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr2:40574400-40574800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:40574400-40575400	Enhancers	Small Intestine	intestine
22	chr2:40574400-40575600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr2:40574600-40575400	Enhancers	Fetal Heart	heart
24	chr2:40574600-40575600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:40574600-40575600	Weak transcription	Adipose Nuclei	Adipose
26	chr2:40574600-40575600	Weak transcription	HSMMtube	muscle
27	chr2:40574600-40575800	Weak transcription	Ovary	ovary
28	chr2:40574600-40575800	Weak transcription	Right Ventricle	heart
29	chr2:40574600-40576800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr2:40574600-40576800	Enhancers	Osteobl	bone
31	chr2:40574600-40579400	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:40574600-40579600	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:40574600-40580000	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr2:40574600-40580000	Weak transcription	Left Ventricle	heart
35	chr2:40574600-40586000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:40574600-40590600	Weak transcription	Aorta	Aorta

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