Variant report

Variant	rs421548
Chromosome Location	chr5:9508979-9508980
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10075682	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs10079862	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10213926	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12657858	0.82[TSI][hapmap]
rs16882871	0.91[CEU][hapmap];0.91[EUR][1000 genomes]
rs169163	0.82[CHD][hapmap];0.81[JPT][hapmap]
rs171992	0.85[CHB][hapmap];0.82[CHD][hapmap]
rs198686	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2135071	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs268469	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268473	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268474	0.85[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs268478	0.84[ASW][hapmap];1.00[CEU][hapmap];0.85[CHD][hapmap];0.94[GIH][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs268493	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268494	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268497	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268499	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268500	0.90[CHB][hapmap];0.81[JPT][hapmap]
rs268501	0.84[CHB][hapmap];0.82[CHD][hapmap]
rs268503	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs268504	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268508	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268510	0.83[CEU][hapmap]
rs268518	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268519	0.85[CHB][hapmap]
rs268520	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs268521	0.85[CHB][hapmap];0.85[CHD][hapmap];0.81[JPT][hapmap]
rs369459	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.94[GIH][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3777359	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs389520	0.83[CHB][hapmap]
rs399271	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs418446	0.85[CHB][hapmap];0.85[CHD][hapmap]
rs422556	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs442173	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs444808	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs446732	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs486947	1.00[CEU][hapmap];0.80[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55667459	0.88[EUR][1000 genomes]
rs55752444	0.88[EUR][1000 genomes]
rs56095432	0.95[EUR][1000 genomes]
rs56326936	0.88[EUR][1000 genomes]
rs570834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs571826	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs62341317	0.91[EUR][1000 genomes]
rs62341320	0.91[EUR][1000 genomes]
rs62342574	0.92[EUR][1000 genomes]
rs62342575	0.86[EUR][1000 genomes]
rs62342577	0.95[EUR][1000 genomes]
rs62342580	0.88[EUR][1000 genomes]
rs62342583	0.88[EUR][1000 genomes]
rs6891680	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs72729173	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv881438	chr5:8728874-9695667	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
2	nsv1015378	chr5:9053542-9617963	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
3	nsv537640	chr5:9053542-9617963	Bivalent/Poised TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
4	nsv597071	chr5:9182376-9760599	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
5	nsv1032672	chr5:9182409-9843893	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1035075	chr5:9182584-9843723	Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv537641	chr5:9182584-9843723	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
8	nsv1034637	chr5:9182784-9741743	Genic enhancers Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv537642	chr5:9182784-9741743	Enhancers Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1028656	chr5:9196001-9837040	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1016885	chr5:9218932-9575594	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
12	nsv1026078	chr5:9222811-9591290	Enhancers ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
13	nsv1022137	chr5:9225121-9745434	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv537643	chr5:9225121-9745434	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
15	nsv1022574	chr5:9314645-9647238	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
16	nsv869120	chr5:9491731-10149255	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv1018275	chr5:9504897-9560199	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
18	nsv537644	chr5:9504897-9560199	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:9478600-9511000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr5:9478600-9515800	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr5:9499200-9528600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr5:9501000-9512400	Weak transcription	Aorta	Aorta
5	chr5:9501200-9512600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr5:9501800-9510600	Weak transcription	Gastric	stomach
7	chr5:9502600-9509400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr5:9503600-9512400	Weak transcription	Fetal Lung	lung
9	chr5:9503600-9519800	Weak transcription	Right Ventricle	heart
10	chr5:9505000-9514000	Weak transcription	Left Ventricle	heart
11	chr5:9505600-9512200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr5:9505800-9512600	Weak transcription	Muscle Satellite Cultured Cells	--
13	chr5:9505800-9522800	Weak transcription	Fetal Kidney	kidney
14	chr5:9505800-9523200	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr5:9506000-9512200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr5:9506000-9512400	Weak transcription	Osteobl	bone
17	chr5:9507400-9510200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr5:9507600-9509000	Enhancers	NHDF-Ad	bronchial
19	chr5:9508200-9509000	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:9508200-9509000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr5:9508200-9509000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:9508200-9509000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr5:9508200-9509000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:9508200-9509000	Enhancers	Fetal Heart	heart
25	chr5:9508200-9509000	Genic enhancers	Fetal Muscle Leg	muscle
26	chr5:9508400-9509000	Genic enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:9508400-9509000	Strong transcription	Fetal Stomach	stomach
28	chr5:9508400-9509000	Enhancers	HSMMtube	muscle
29	chr5:9508400-9512400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr5:9508600-9509000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr5:9508600-9509200	Strong transcription	Rectal Mucosa Donor 29	rectum
32	chr5:9508600-9512800	Weak transcription	Pancreas	Pancrea
33	chr5:9508800-9510000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:9508800-9512800	Weak transcription	NHLF	lung
35	chr5:9508800-9514200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr5:9508800-9516200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr5:9508800-9520000	Weak transcription	Fetal Muscle Trunk	muscle
38	chr5:9508800-9520000	Weak transcription	Placenta Amnion	Placenta Amnion

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