Variant report

Variant	rs247237
Chromosome Location	chr5:61746142-61746143
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	chr5:61698166..61701072-chr5:61746035..61747644,2	K562	blood:

Variant related genes	Relation type
ENSG00000086189	Chromatin interaction
ENSG00000086200	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10058598	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10060044	0.80[AMR][1000 genomes]
rs10062387	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs10067200	0.83[CEU][hapmap];1.00[CHB][hapmap]
rs10069594	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10069988	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10077586	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs101091	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10461472	0.82[CHB][hapmap]
rs12517326	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12659793	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs12659814	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap]
rs1301064	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1301065	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361143	0.82[CHB][hapmap]
rs1477358	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs149540	0.85[CHD][hapmap]
rs152184	0.85[CHD][hapmap]
rs152186	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152191	0.85[CHD][hapmap]
rs152192	0.85[CHD][hapmap]
rs152199	0.85[CHD][hapmap]
rs152204	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152205	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152210	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152215	0.85[CHD][hapmap]
rs1562244	0.85[CHD][hapmap]
rs16890622	0.81[CHB][hapmap]
rs16890800	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs174647	0.82[CHB][hapmap]
rs1995782	0.85[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap]
rs2289883	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs2344395	0.80[ASW][hapmap];0.88[MEX][hapmap]
rs247225	0.87[ASN][1000 genomes]
rs247227	0.87[ASN][1000 genomes]
rs247231	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247232	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247233	0.81[CHD][hapmap]
rs247240	0.85[CHD][hapmap]
rs247241	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs247242	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247243	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247244	0.83[CHD][hapmap]
rs247250	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247251	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247254	0.87[ASN][1000 genomes]
rs247259	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247262	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247264	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs247265	0.82[CHB][hapmap]
rs247266	0.87[ASN][1000 genomes]
rs247270	0.83[CHD][hapmap]
rs247479	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs264530	0.85[CHD][hapmap]
rs26635	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs26637	0.85[CHD][hapmap]
rs26639	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs26642	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27089	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs27448	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs27449	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs27693	0.85[CHD][hapmap]
rs27931	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35119	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35202928	0.80[AMR][1000 genomes]
rs3776638	0.85[CHD][hapmap]
rs3822485	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3846467	0.85[CEU][hapmap];1.00[CHB][hapmap]
rs4145851	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap]
rs4441833	0.82[CHB][hapmap]
rs4700494	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.89[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes]
rs6881888	0.85[CHD][hapmap]
rs767159	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7702634	0.81[CHB][hapmap]
rs7717128	0.85[CHD][hapmap]
rs7717143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.80[AMR][1000 genomes]
rs7722692	0.85[CHD][hapmap]
rs7729526	0.85[CHD][hapmap]
rs7737525	0.88[CHD][hapmap]
rs784916	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs784918	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs959899	0.85[CHD][hapmap]
rs9632387	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024090	chr5:61258759-61921150	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv2759345	chr5:61403138-61748912	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1020255	chr5:61451792-62031365	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv1027539	chr5:61457762-62000008	Weak transcription Strong transcription Genic enhancers Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv1033578	chr5:61606610-61911153	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
6	nsv1025145	chr5:61624735-61824265	Enhancers Strong transcription Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1029708	chr5:61625813-61877628	Bivalent/Poised TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
8	nsv881728	chr5:61630879-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
9	esv2757117	chr5:61649403-61748912	Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
10	nsv598348	chr5:61650843-61895124	Weak transcription Strong transcription ZNF genes & repeats Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
11	esv35035	chr5:61657943-61792243	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv881729	chr5:61719506-61857577	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs247237	DIMT1L	cis	cerebellum	SCAN
rs247237	NEU2	trans	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61709200-61770800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:61709400-61763400	Weak transcription	Aorta	Aorta
3	chr5:61709800-61746600	Weak transcription	Fetal Thymus	thymus
4	chr5:61709800-61769000	Weak transcription	NH-A	brain
5	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr5:61714000-61746600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:61715000-61747200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr5:61722800-61770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr5:61725800-61747200	Weak transcription	Thymus	Thymus
10	chr5:61726200-61746200	Weak transcription	HUVEC	blood vessel
11	chr5:61726400-61747200	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr5:61728200-61746800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr5:61728200-61752800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr5:61728400-61747400	Weak transcription	Osteobl	bone
15	chr5:61728400-61748200	Weak transcription	Lung	lung
16	chr5:61728400-61752800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr5:61728400-61763400	Weak transcription	Pancreas	Pancrea
18	chr5:61728400-61807600	Weak transcription	Psoas Muscle	Psoas
19	chr5:61728800-61746800	Weak transcription	HSMMtube	muscle
20	chr5:61728800-61748200	Weak transcription	Fetal Lung	lung
21	chr5:61728800-61763000	Weak transcription	Fetal Brain Female	brain
22	chr5:61728800-61838200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
23	chr5:61729400-61746200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr5:61729600-61746200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr5:61729600-61747400	Weak transcription	Right Ventricle	heart
26	chr5:61729600-61752800	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr5:61729800-61746200	Weak transcription	HSMM	muscle
28	chr5:61730000-61748000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:61730000-61834200	Weak transcription	Gastric	stomach
30	chr5:61730200-61747200	Weak transcription	Left Ventricle	heart
31	chr5:61730200-61747600	Weak transcription	Brain Anterior Caudate	brain
32	chr5:61730800-61747200	Weak transcription	Ovary	ovary
33	chr5:61730800-61750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr5:61731800-61764000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr5:61732200-61753200	Weak transcription	NHLF	lung
36	chr5:61732800-61805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr5:61733200-61747400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr5:61733200-61756800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr5:61733600-61763000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr5:61738800-61763000	Weak transcription	Stomach Smooth Muscle	stomach
41	chr5:61739200-61747200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr5:61739200-61763000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr5:61739200-61763400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr5:61739200-61862800	Weak transcription	Brain Substantia Nigra	brain
45	chr5:61739400-61746200	Weak transcription	Fetal Kidney	kidney
46	chr5:61739600-61746200	Weak transcription	Liver	Liver
47	chr5:61739600-61746200	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr5:61739600-61746200	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr5:61739600-61747200	Weak transcription	Cortex derived primary cultured neurospheres	brain
50	chr5:61739600-61787800	Weak transcription	Brain Cingulate Gyrus	brain

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