Variant report

Variant	rs17817455
Chromosome Location	chr6:55928776-55928777
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	E2F4	chr6:55928686-55928857	MCF10A-Er-Src	breast:	n/a	n/a
2	MAX	chr6:55928721-55928858	NB4	blood:	n/a	chr6:55928802-55928812

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:55926997..55929020-chr6:55932279..55934927,2	MCF-7	breast:

Variant related genes	Relation type
COL21A1	TF binding region

Extended variants
information (count: 120 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:113)

rs_ID	r²[population]
rs1028390	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10484704	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10484724	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10807507	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10807508	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10807510	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10948974	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10948975	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12189567	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12189571	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12190695	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12190930	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12191931	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12192012	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12194051	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs12194192	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12194397	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12194916	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12194997	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12195340	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12196213	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12196526	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12196649	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12196670	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12196709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12196860	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12197951	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12201286	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12201413	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12201531	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12203179	0.89[JPT][hapmap];0.81[MEX][hapmap]
rs12203653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12203768	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12205230	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12205653	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12206920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12207120	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12207662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12207665	1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs12207715	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12207719	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs12208500	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208615	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208823	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208954	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12209003	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12209420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12209529	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12210228	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12210402	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12211223	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212135	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12212211	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12212998	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12213291	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12213571	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12214594	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12214662	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12215027	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs12215913	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12216538	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1555095	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs1555096	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs16887615	1.00[CEU][hapmap];0.85[CHB][hapmap]
rs17218267	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17218309	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17218770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17219028	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs17219063	1.00[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs17219126	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17219382	0.85[CHB][hapmap];0.86[CHD][hapmap];0.92[GIH][hapmap];0.89[JPT][hapmap]
rs17221026	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs17223058	1.00[CEU][hapmap];0.85[CHB][hapmap];0.92[GIH][hapmap];0.86[TSI][hapmap]
rs17683841	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17683846	1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap]
rs17683955	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17751067	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17751085	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17751114	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs17751143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17817377	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17817407	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17817730	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818151	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818687	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17819585	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes]
rs17819753	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs17819824	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes]
rs1925178	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.90[MEX][hapmap];0.91[TSI][hapmap]
rs2076474	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2076475	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2143359	0.87[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes]
rs2894833	0.94[ASN][1000 genomes]
rs35471617	0.81[AMR][1000 genomes]
rs3950155	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs41464152	1.00[CHB][hapmap];0.85[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs4295483	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4295484	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4336432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4388288	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4452633	1.00[JPT][hapmap]
rs4469280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4482975	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4544908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs57122743	0.85[AMR][1000 genomes]
rs59186267	0.81[AMR][1000 genomes]
rs60913237	0.85[AMR][1000 genomes]
rs62412804	0.81[ASN][1000 genomes]
rs7450492	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs763966	1.00[CEU][hapmap];0.85[CHB][hapmap];0.82[AMR][1000 genomes]
rs9382577	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1034037	chr6:55222409-56069600	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv885911	chr6:55789704-56143231	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv526703	chr6:55810482-56023811	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1023687	chr6:55868611-55940255	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv1020208	chr6:55870429-55932120	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv538227	chr6:55870429-55932120	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases
7	nsv1029182	chr6:55910866-55991956	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:55911800-55940800	Weak transcription	Left Ventricle	heart
2	chr6:55920600-56018400	Weak transcription	Ovary	ovary
3	chr6:55921000-55929200	Weak transcription	Right Ventricle	heart
4	chr6:55921000-55930000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:55922600-55940800	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:55925000-55933400	Weak transcription	Colon Smooth Muscle	Colon
7	chr6:55925600-55946200	Weak transcription	Fetal Kidney	kidney
8	chr6:55927800-55929400	Strong transcription	Stomach Smooth Muscle	stomach
9	chr6:55927800-55931000	Strong transcription	Fetal Lung	lung
10	chr6:55928000-55929200	Strong transcription	Fetal Muscle Trunk	muscle
11	chr6:55928200-55930600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:55928200-55931600	Weak transcription	Fetal Stomach	stomach
13	chr6:55928400-55929000	Genic enhancers	Aorta	Aorta
14	chr6:55928600-55930600	Strong transcription	Fetal Heart	heart

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