Variant report

Variant	rs975602
Chromosome Location	chr12:41615499-41615500
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:41615335..41618133-chr12:41621079..41623279,2	K562	blood:

Extended variants
information (count: 80 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:75)

rs_ID	r²[population]
rs10506182	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs10748267	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10748275	0.84[EUR][1000 genomes]
rs10785165	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs10785174	0.84[EUR][1000 genomes]
rs10785177	0.85[CEU][hapmap];0.82[GIH][hapmap]
rs10785186	0.91[CHB][hapmap]
rs10879831	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10879858	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10879867	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10879889	0.88[CEU][hapmap];0.80[EUR][1000 genomes]
rs11180421	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs11180448	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs12829840	0.86[ASN][1000 genomes]
rs1367600	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs1367602	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1405548	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1431104	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431110	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1431111	0.81[EUR][1000 genomes]
rs1431112	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];1.00[ASN][1000 genomes]
rs1431113	0.81[CEU][hapmap];0.82[EUR][1000 genomes]
rs1431114	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs1431115	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs1431116	0.83[EUR][1000 genomes]
rs1461094	0.92[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1527086	1.00[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1852461	0.85[CEU][hapmap];0.82[GIH][hapmap];0.86[MEX][hapmap];0.84[EUR][1000 genomes]
rs1864611	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1864613	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1870704	0.85[CEU][hapmap];0.85[MEX][hapmap];0.83[EUR][1000 genomes]
rs1966609	0.81[CEU][hapmap];0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs2043134	0.81[CEU][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs2060053	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2060054	0.83[EUR][1000 genomes]
rs2060055	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2163415	0.85[EUR][1000 genomes]
rs2163416	1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs2169299	0.86[EUR][1000 genomes]
rs2195706	0.80[EUR][1000 genomes]
rs281832	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs281837	0.80[EUR][1000 genomes]
rs281839	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs281840	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs281841	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs281843	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2897228	0.80[EUR][1000 genomes]
rs3847980	0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3847981	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3858726	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4238081	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4278570	0.81[EUR][1000 genomes]
rs4767999	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4768334	1.00[CHB][hapmap];0.82[JPT][hapmap];0.91[ASN][1000 genomes]
rs4768335	0.81[CEU][hapmap];0.86[MEX][hapmap];0.85[EUR][1000 genomes]
rs6582240	0.94[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6582280	0.80[EUR][1000 genomes]
rs6582281	0.80[EUR][1000 genomes]
rs6582282	0.80[EUR][1000 genomes]
rs6582283	0.80[EUR][1000 genomes]
rs7137842	0.80[EUR][1000 genomes]
rs7301200	0.82[EUR][1000 genomes]
rs7303285	0.94[ASW][hapmap];0.92[CEU][hapmap];0.84[CHD][hapmap];0.92[GIH][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap];0.94[MKK][hapmap];0.89[TSI][hapmap];0.93[YRI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7304286	0.84[EUR][1000 genomes]
rs7305919	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[JPT][hapmap];0.94[ASN][1000 genomes]
rs7342366	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs776560	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs776561	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs776562	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs776567	0.81[EUR][1000 genomes]
rs7954881	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7956699	0.82[EUR][1000 genomes]
rs7961657	0.80[EUR][1000 genomes]
rs7963760	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.90[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9788073	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv497867	chr12:41286305-41728650	Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv427910	chr12:41374913-41650593	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv1051524	chr12:41409977-41643387	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv899034	chr12:41515090-41698342	Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv899035	chr12:41548545-41710912	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs975602	CNTN1	cis	cerebellum	SCAN

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:41611800-41625200	Weak transcription	Aorta	Aorta
2	chr12:41612200-41615800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr12:41613000-41615800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
4	chr12:41613800-41616000	Enhancers	Ovary	ovary
5	chr12:41613800-41618000	Enhancers	Primary hematopoietic stem cells	blood
6	chr12:41614000-41615600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr12:41614000-41616000	Enhancers	Rectal Smooth Muscle	rectum
8	chr12:41614000-41616200	Enhancers	Colon Smooth Muscle	Colon
9	chr12:41614200-41616200	Enhancers	Primary hematopoietic stem cells short term culture	blood
10	chr12:41615000-41615800	Weak transcription	Spleen	Spleen
11	chr12:41615000-41616000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:41615000-41617600	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:41615200-41617400	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr12:41615200-41617800	Weak transcription	HUES6 Cell Line	embryonic stem cell

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