Variant report

Variant	rs27448
Chromosome Location	chr5:61764813-61764814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 94 )
Associated
traits (count: 0)

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];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10060044	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10062387	1.00[CHB][hapmap]
rs10067200	1.00[CHB][hapmap]
rs10069594	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];0.83[JPT][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs10069988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10077586	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs10079618	0.81[AMR][1000 genomes]
rs101091	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10461472	0.82[CHB][hapmap]
rs12517326	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12659793	1.00[CHB][hapmap]
rs12659814	1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap]
rs1301064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.98[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1301065	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13361143	0.82[CHB][hapmap]
rs1477358	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs149540	0.85[CHD][hapmap]
rs152184	0.85[CHD][hapmap]
rs152186	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs152191	0.85[CHD][hapmap]
rs152192	0.85[CHD][hapmap]
rs152199	0.85[CHD][hapmap]
rs152204	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152205	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs152210	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs152215	0.85[CHD][hapmap]
rs1562244	0.85[CHD][hapmap]
rs16890622	0.81[CHB][hapmap]
rs16890800	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs174647	0.82[CHB][hapmap]
rs2289883	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs247225	0.86[ASN][1000 genomes]
rs247227	0.86[ASN][1000 genomes]
rs247231	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247232	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs247233	0.81[CHD][hapmap]
rs247237	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]
rs247240	0.85[CHD][hapmap]
rs247241	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs247242	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247243	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247244	0.83[CHD][hapmap]
rs247250	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs247251	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs247254	0.86[ASN][1000 genomes]
rs247259	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs247262	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs247264	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs247265	0.82[CHB][hapmap]
rs247266	0.86[ASN][1000 genomes]
rs247270	0.83[CHD][hapmap]
rs247479	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.87[LWK][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs264530	0.85[CHD][hapmap]
rs26635	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs26637	0.85[CHD][hapmap]
rs26639	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs26642	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27089	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs27449	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs27693	0.85[CHD][hapmap]
rs27931	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35119	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[LWK][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35202928	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3776638	0.85[CHD][hapmap]
rs3822485	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs3846467	1.00[CHB][hapmap]
rs4145851	1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.83[JPT][hapmap];0.83[TSI][hapmap]
rs4441833	0.82[CHB][hapmap]
rs4700494	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs57199871	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6881888	0.85[CHD][hapmap]
rs767159	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7702634	0.81[CHB][hapmap]
rs7717128	0.85[CHD][hapmap]
rs7717143	0.96[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.82[AMR][1000 genomes]
rs7722692	0.85[CHD][hapmap]
rs7729526	0.85[CHD][hapmap]
rs7737525	0.88[CHD][hapmap]
rs784916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs784918	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs959899	0.85[CHD][hapmap]
rs9632387	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv881730	chr5:61750667-61883581	Weak transcription Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

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	chr5:61709800-61769000	Weak transcription	NH-A	brain
3	chr5:61709800-61809200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr5:61722800-61770600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr5:61728400-61807600	Weak transcription	Psoas Muscle	Psoas
6	chr5:61728800-61838200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr5:61730000-61834200	Weak transcription	Gastric	stomach
8	chr5:61732800-61805200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:61739200-61862800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:61739600-61787800	Weak transcription	Brain Cingulate Gyrus	brain
11	chr5:61744800-61838600	Weak transcription	Colonic Mucosa	Colon
12	chr5:61746200-61783600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr5:61748000-61794600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:61748000-61862800	Weak transcription	Right Ventricle	heart
15	chr5:61748600-61784400	Weak transcription	Lung	lung
16	chr5:61748600-61787000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr5:61748800-61771400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr5:61749000-61786200	Weak transcription	Brain Anterior Caudate	brain
19	chr5:61749400-61779400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr5:61750600-61785200	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr5:61750600-61786000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
22	chr5:61752600-61774000	Weak transcription	Fetal Stomach	stomach
23	chr5:61753400-61774600	Weak transcription	Brain Germinal Matrix	brain
24	chr5:61757600-61792200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr5:61758800-61890000	Weak transcription	Small Intestine	intestine
26	chr5:61759000-61834200	Weak transcription	Esophagus	oesophagus
27	chr5:61759800-61790000	Weak transcription	Primary neutrophils fromperipheralblood	blood
28	chr5:61760600-61781400	Weak transcription	Fetal Intestine Small	intestine
29	chr5:61760800-61847200	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:61761600-61768000	Strong transcription	Dnd41	blood
31	chr5:61762000-61769000	Weak transcription	HMEC	breast
32	chr5:61762200-61768800	Weak transcription	HUVEC	blood vessel
33	chr5:61762200-61776600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr5:61762400-61765600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr5:61762400-61766000	Strong transcription	Monocytes-CD14+_RO01746	blood
36	chr5:61762400-61766400	Strong transcription	Primary B cells from peripheral blood	blood
37	chr5:61762400-61767000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr5:61762400-61770600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:61762600-61765600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr5:61762600-61766400	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:61762600-61767000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr5:61762800-61766200	Strong transcription	Liver	Liver
43	chr5:61762800-61766400	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr5:61762800-61766400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr5:61762800-61766400	Strong transcription	Primary B cells from cord blood	blood
46	chr5:61762800-61766400	Strong transcription	Primary T cells from cord blood	blood
47	chr5:61763000-61765000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr5:61763000-61765400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr5:61763000-61765600	Strong transcription	HUES6 Cell Line	embryonic stem cell
50	chr5:61763000-61765600	Strong transcription	Primary T helper cells PMA-I stimulated	--

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