Variant report

Variant	rs247254
Chromosome Location	chr5:61676911-61676912
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:61671360..61674176-chr5:61674605..61678360,3	MCF-7	breast:
2	chr5:61675162..61677074-chr5:61689964..61691890,2	MCF-7	breast:
3	chr5:61675578..61677297-chr5:61689540..61692147,2	K562	blood:

Extended variants
information (count: 122 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:108)

rs_ID	r²[population]
rs10051719	0.83[AFR][1000 genomes]
rs10058598	0.84[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs10062387	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs10067200	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes]
rs10069988	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs10075026	0.84[AFR][1000 genomes]
rs101091	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs10461472	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs10471546	0.81[ASN][1000 genomes]
rs10939937	0.82[ASN][1000 genomes]
rs12515967	0.81[ASN][1000 genomes]
rs12517326	0.85[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap]
rs12655269	0.83[AFR][1000 genomes]
rs12659793	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs12659814	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes]
rs12696990	0.81[ASN][1000 genomes]
rs1301064	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.84[ASN][1000 genomes]
rs1301065	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs1309156	0.84[ASN][1000 genomes]
rs13361143	0.82[CHB][hapmap]
rs13361219	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs149540	0.85[CHD][hapmap]
rs152184	0.85[CHD][hapmap]
rs152186	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs152191	0.85[CHD][hapmap]
rs152192	0.85[CHD][hapmap]
rs152199	0.85[CHD][hapmap]
rs152204	0.89[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs152205	0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs152210	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs152215	0.85[CHD][hapmap]
rs1562244	0.85[CHD][hapmap]
rs16890622	0.81[CHB][hapmap]
rs174647	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs1862527	0.86[AFR][1000 genomes]
rs1995782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AFR][1000 genomes]
rs2289883	0.82[CHB][hapmap];0.88[CHD][hapmap];0.84[ASN][1000 genomes]
rs2344395	0.81[CEU][hapmap];0.88[MEX][hapmap]
rs247218	0.84[ASN][1000 genomes]
rs247220	0.82[ASN][1000 genomes]
rs247221	0.83[ASN][1000 genomes]
rs247222	0.84[ASN][1000 genomes]
rs247223	0.83[ASN][1000 genomes]
rs247225	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247227	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247231	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs247232	0.87[ASN][1000 genomes]
rs247233	0.81[CHD][hapmap]
rs247237	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs247240	0.85[CHD][hapmap]
rs247241	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs247242	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247243	0.83[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247244	0.83[CHD][hapmap]
rs247250	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs247251	0.81[CEU][hapmap];0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs247255	0.81[ASN][1000 genomes]
rs247259	0.91[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs247262	0.90[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs247264	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs247265	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs247266	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs247267	0.84[ASN][1000 genomes]
rs247268	0.82[ASN][1000 genomes]
rs247269	0.84[ASN][1000 genomes]
rs247270	0.83[CHD][hapmap]
rs247273	0.84[ASN][1000 genomes]
rs247275	0.84[ASN][1000 genomes]
rs247479	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs264519	0.81[ASN][1000 genomes]
rs264521	0.81[ASN][1000 genomes]
rs264523	0.81[ASN][1000 genomes]
rs264528	0.81[ASN][1000 genomes]
rs264530	0.85[CHD][hapmap]
rs264531	0.81[ASN][1000 genomes]
rs26635	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.84[ASN][1000 genomes]
rs26637	0.85[CHD][hapmap]
rs26639	0.82[ASN][1000 genomes]
rs26642	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.82[ASN][1000 genomes]
rs27089	0.90[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs27448	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs27449	0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs27693	0.85[CHD][hapmap]
rs27931	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28589513	0.83[AFR][1000 genomes]
rs35119	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.86[ASN][1000 genomes]
rs35348760	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3776615	0.81[ASN][1000 genomes]
rs3776638	0.85[CHD][hapmap]
rs3822485	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3846467	0.96[CEU][hapmap];1.00[CHB][hapmap];0.84[AFR][1000 genomes]
rs4145851	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs438143	0.82[ASN][1000 genomes]
rs4441833	0.82[CHB][hapmap]
rs4700009	0.81[ASN][1000 genomes]
rs56049450	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs56317447	0.83[AFR][1000 genomes]
rs6449593	0.85[CEU][hapmap]
rs6881888	0.85[CHD][hapmap]
rs767159	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.81[TSI][hapmap];0.81[ASN][1000 genomes]
rs7700569	0.81[ASN][1000 genomes]
rs7702634	0.81[CHB][hapmap];0.81[ASN][1000 genomes]
rs7722692	0.85[CHD][hapmap]
rs7737525	0.88[CHD][hapmap]
rs784916	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs784918	0.87[ASN][1000 genomes]
rs9291758	0.81[ASN][1000 genomes]
rs959899	0.85[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 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	esv2757996	chr5:61403138-61687817	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv881726	chr5:61556730-61676911	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
7	nsv881727	chr5:61578041-61700970	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region miRNA target site	23 gene(s)	inside rSNPs	diseases
8	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
9	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
10	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
11	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
12	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
13	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
14	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs247254	DIMT1L	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:61639800-61684200	Weak transcription	Psoas Muscle	Psoas
2	chr5:61641400-61682400	Weak transcription	Fetal Heart	heart
3	chr5:61642400-61697400	Strong transcription	HUES64 Cell Line	embryonic stem cell
4	chr5:61642600-61688400	Weak transcription	Right Ventricle	heart
5	chr5:61642600-61696000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr5:61642600-61699200	Weak transcription	Gastric	stomach
7	chr5:61643000-61697000	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr5:61643800-61680600	Strong transcription	Placenta	Placenta
9	chr5:61644000-61689000	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr5:61645400-61689200	Strong transcription	Primary T helper cells fromperipheralblood	blood
11	chr5:61647000-61690000	Weak transcription	Spleen	Spleen
12	chr5:61647600-61698000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr5:61656200-61698000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
14	chr5:61656800-61687800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr5:61658400-61691800	Strong transcription	Dnd41	blood
16	chr5:61659800-61695800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr5:61661000-61678600	Strong transcription	Fetal Thymus	thymus
18	chr5:61661800-61680000	Weak transcription	Colonic Mucosa	Colon
19	chr5:61661800-61698000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr5:61662000-61697800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr5:61664200-61678400	Strong transcription	Fetal Intestine Large	intestine
23	chr5:61664600-61689200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr5:61665400-61699000	Weak transcription	Esophagus	oesophagus
25	chr5:61665600-61688000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:61666600-61678600	Strong transcription	Primary T cells from cord blood	blood
27	chr5:61666600-61679000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr5:61666800-61679200	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr5:61666800-61698000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
30	chr5:61667000-61691200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr5:61667000-61691600	Strong transcription	Monocytes-CD14+_RO01746	blood
32	chr5:61667000-61697200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr5:61667400-61677800	Strong transcription	GM12878-XiMat	blood
34	chr5:61667400-61678400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr5:61667400-61697200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:61667600-61697800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr5:61667600-61698000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr5:61667800-61681400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr5:61668000-61677400	Strong transcription	HSMM	muscle
40	chr5:61668000-61698000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr5:61668200-61678400	Strong transcription	Rectal Mucosa Donor 31	rectum
42	chr5:61668400-61685600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr5:61668600-61697000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr5:61669200-61690200	Strong transcription	HUVEC	blood vessel
45	chr5:61669400-61677400	Strong transcription	NHDF-Ad	bronchial
46	chr5:61669400-61677800	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr5:61669400-61678000	Strong transcription	Adipose Nuclei	Adipose
48	chr5:61669400-61678000	Strong transcription	Duodenum Mucosa	Duodenum
49	chr5:61669400-61678000	Strong transcription	Fetal Muscle Leg	muscle
50	chr5:61669400-61678200	Strong transcription	Rectal Mucosa Donor 29	rectum

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