Variant report

Variant	rs2547917
Chromosome Location	chr5:58713680-58713681
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10065206	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10214073	0.81[AMR][1000 genomes]
rs1445918	0.86[CEU][hapmap];0.88[EUR][1000 genomes]
rs2547918	0.92[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs2547920	0.86[EUR][1000 genomes]
rs2591744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2591747	0.85[EUR][1000 genomes]
rs2591749	0.91[EUR][1000 genomes]
rs2591751	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2607340	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2607344	0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2607347	1.00[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2702363	0.93[CEU][hapmap];0.85[CHB][hapmap];0.88[YRI][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2702371	1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[ASN][1000 genomes]
rs2702375	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2702376	0.90[AFR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2702377	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[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	nsv1023628	chr5:58557950-58757438	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
2	nsv917274	chr5:58565291-58814374	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
3	nsv1030716	chr5:58636116-58718362	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	nsv881705	chr5:58668669-58745872	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv1028022	chr5:58673780-58786468	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv1034656	chr5:58674724-58755580	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv598253	chr5:58675538-58754510	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Adverse response to chemotherapy (neutropenia/leucopenia) (gemcitabine)	23648065	GWAS catalog

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58704200-58714200	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr5:58705600-58751400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr5:58707600-58714800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:58708600-58718200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:58709800-58756800	Weak transcription	Aorta	Aorta
6	chr5:58710400-58714200	Weak transcription	Fetal Intestine Large	intestine
7	chr5:58710800-58714400	Weak transcription	Fetal Muscle Leg	muscle
8	chr5:58712200-58714400	Enhancers	A549	lung
9	chr5:58712400-58714600	Weak transcription	Skeletal Muscle Male	skeletal muscle
10	chr5:58712400-58719600	Weak transcription	Psoas Muscle	Psoas
11	chr5:58712600-58717800	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr5:58712600-58718000	Weak transcription	Fetal Lung	lung
13	chr5:58713000-58715200	Enhancers	Duodenum Mucosa	Duodenum
14	chr5:58713200-58715000	Enhancers	Colon Smooth Muscle	Colon
15	chr5:58713400-58715200	Enhancers	Fetal Intestine Small	intestine
16	chr5:58713600-58714400	Weak transcription	Small Intestine	intestine

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

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