Variant report

Variant	rs6680219
Chromosome Location	chr1:57637298-57637299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10789044	0.84[AMR][1000 genomes]
rs10789045	0.84[AMR][1000 genomes]
rs10889026	0.84[AMR][1000 genomes]
rs10889027	0.81[EUR][1000 genomes]
rs10889030	0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs12034636	0.84[AMR][1000 genomes]
rs12120310	0.84[AMR][1000 genomes]
rs12123599	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1413226	0.80[TSI][hapmap];0.82[AMR][1000 genomes]
rs1504588	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1504589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs155287	0.87[EUR][1000 genomes]
rs155288	0.87[TSI][hapmap];0.87[EUR][1000 genomes]
rs155312	1.00[CHB][hapmap]
rs17482565	0.88[AMR][1000 genomes]
rs17541356	1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs17541479	0.89[ASW][hapmap];0.93[LWK][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs1831870	0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs197110	1.00[CHB][hapmap]
rs4912429	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];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912430	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4912431	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4912432	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55944821	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6670988	0.88[AMR][1000 genomes]
rs7544837	0.80[EUR][1000 genomes]
rs7548633	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7552759	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];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869295	chr1:56894955-57656562	Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv461628	chr1:57463326-57816489	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv546305	chr1:57463326-57816489	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57624000-57644800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr1:57632000-57637400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:57632000-57637800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr1:57633400-57639800	Weak transcription	Fetal Intestine Large	intestine
5	chr1:57636000-57637800	Enhancers	HUES48 Cell Line	embryonic stem cell
6	chr1:57636400-57637600	Enhancers	H1 Cell Line	embryonic stem cell
7	chr1:57636400-57637800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:57636400-57637800	Enhancers	iPS-18 Cell Line	embryonic stem cell
9	chr1:57636600-57637800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:57636600-57638000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:57636600-57638200	Enhancers	H9 Cell Line	embryonic stem cell
12	chr1:57636600-57638800	Enhancers	HUES64 Cell Line	embryonic stem cell
13	chr1:57636600-57641400	Weak transcription	Fetal Intestine Small	intestine
14	chr1:57636800-57637400	Enhancers	HUES6 Cell Line	embryonic stem cell
15	chr1:57636800-57637400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr1:57636800-57637800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr1:57637000-57637600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr1:57637000-57638000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr1:57637200-57637400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links