Variant report

Variant	rs6543605
Chromosome Location	chr2:31354270-31354271
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10190164	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs10201005	0.93[JPT][hapmap]
rs11675787	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11684970	0.87[ASN][1000 genomes]
rs12105231	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12989636	0.90[CEU][hapmap];0.94[JPT][hapmap];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13408448	0.80[ASN][1000 genomes]
rs1562023	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17010764	0.87[CEU][hapmap];0.80[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2008535	0.81[CEU][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57938947	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs59588353	0.89[ASN][1000 genomes]
rs60245472	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6543606	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6543607	0.94[JPT][hapmap];0.83[ASN][1000 genomes]
rs6543609	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs6706156	0.94[JPT][hapmap]
rs6708641	0.83[ASN][1000 genomes]
rs6743542	0.90[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.93[TSI][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6747497	0.90[CEU][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.80[TSI][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs7560152	0.95[CEU][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7560583	0.91[ASN][1000 genomes]
rs7564367	0.83[ASN][1000 genomes]
rs7596724	0.94[JPT][hapmap]
rs956747	0.91[CEU][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948552	chr2:31118599-31595424	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:31347800-31358800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr2:31349400-31354400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr2:31349600-31355000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:31349600-31355600	Weak transcription	HMEC	breast
5	chr2:31349800-31354400	Weak transcription	NHEK	skin
6	chr2:31349800-31355400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr2:31349800-31357200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr2:31350000-31355200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:31350000-31359600	Weak transcription	Pancreas	Pancrea
10	chr2:31350200-31355800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr2:31351600-31358600	Weak transcription	Primary neutrophils fromperipheralblood	blood
12	chr2:31351600-31359600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr2:31351800-31355400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:31352200-31354400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr2:31352400-31356000	Enhancers	H1 Cell Line	embryonic stem cell
16	chr2:31352600-31355600	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr2:31353000-31356000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr2:31353200-31354400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr2:31353200-31354400	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr2:31353200-31355200	Weak transcription	H9 Cell Line	embryonic stem cell
21	chr2:31353400-31354400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:31353400-31354400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr2:31353400-31358600	Enhancers	Brain Germinal Matrix	brain
24	chr2:31353400-31359600	Weak transcription	Spleen	Spleen
25	chr2:31354000-31354400	Weak transcription	Fetal Brain Male	brain
26	chr2:31354000-31355600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr2:31354000-31355800	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr2:31354200-31355000	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr2:31354200-31355600	Enhancers	iPS-18 Cell Line	embryonic stem cell
30	chr2:31354200-31355800	Enhancers	HUES48 Cell Line	embryonic stem cell
31	chr2:31354200-31356000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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