Variant report

Variant	rs6688120
Chromosome Location	chr1:217206190-217206191
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1004626	0.92[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs10863289	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11117756	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs11807917	0.92[CEU][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs1416531	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17636912	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs1890554	0.85[CHD][hapmap];0.84[ASN][1000 genomes]
rs2789552	0.84[ASN][1000 genomes]
rs4085455	0.96[CEU][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4846804	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61816725	0.85[EUR][1000 genomes]
rs61816726	0.85[EUR][1000 genomes]
rs6694626	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7538474	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv428610	chr1:217143317-217307243	Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1008670	chr1:217155114-217206765	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	nsv1012243	chr1:217157000-217206765	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv1006155	chr1:217157000-217215465	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	nsv1004880	chr1:217157748-217206765	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	nsv1011212	chr1:217162443-217206765	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv549205	chr1:217165548-217270219	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217194800-217206200	Weak transcription	Left Ventricle	heart
2	chr1:217196000-217206200	Weak transcription	Right Atrium	heart
3	chr1:217196200-217206200	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:217199600-217206200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr1:217199600-217211800	Weak transcription	Gastric	stomach
6	chr1:217204000-217212000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr1:217204200-217207800	Weak transcription	Pancreas	Pancrea
8	chr1:217204200-217209800	Weak transcription	Fetal Muscle Leg	muscle
9	chr1:217204800-217226000	Weak transcription	Fetal Kidney	kidney
10	chr1:217205400-217209600	Weak transcription	Fetal Intestine Small	intestine
11	chr1:217205600-217206600	Enhancers	Brain Substantia Nigra	brain
12	chr1:217206000-217206800	Enhancers	Fetal Heart	heart

Quick Search:

Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

what's new

Quick links