Variant report

Variant	rs17797601
Chromosome Location	chr5:58818633-58818634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58806024..58808912-chr5:58817531..58819530,2	MCF-7	breast:

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10514860	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11949561	1.00[CEU][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187079	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12187448	0.83[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17728654	1.00[JPT][hapmap]
rs17740749	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17740767	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741233	0.83[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17795596	1.00[JPT][hapmap]
rs17795692	1.00[JPT][hapmap]
rs17796040	1.00[JPT][hapmap]
rs17796824	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2081093	0.84[CEU][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2098699	1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4326095	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4551023	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56075449	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56396168	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861969	0.84[CEU][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs72767794	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767801	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72767802	0.85[EUR][1000 genomes]
rs72769704	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7717821	1.00[JPT][hapmap]
rs7729912	1.00[JPT][hapmap]
rs7737908	1.00[JPT][hapmap]

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	nsv598254	chr5:58715782-58923601	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv881706	chr5:58730111-58865857	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv1031631	chr5:58783629-59015470	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region miRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58804800-58819800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr5:58810000-58823600	Weak transcription	Colon Smooth Muscle	Colon
3	chr5:58813600-58818800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr5:58814400-58820400	Weak transcription	Psoas Muscle	Psoas
5	chr5:58814600-58823800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr5:58815400-58830400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:58815600-58821400	Weak transcription	HUVEC	blood vessel
8	chr5:58815800-58823600	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr5:58817000-58819000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr5:58817200-58818800	Enhancers	Fetal Intestine Large	intestine
11	chr5:58817400-58818800	Enhancers	Fetal Intestine Small	intestine
12	chr5:58817400-58820800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr5:58818200-58819000	Enhancers	Placenta Amnion	Placenta Amnion
14	chr5:58818400-58818800	Transcr. at gene 5' and 3'	A549	lung
15	chr5:58818400-58819200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
16	chr5:58818400-58819600	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr5:58818400-58820400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr5:58818400-58822400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr5:58818600-58818800	Enhancers	Rectal Mucosa Donor 29	rectum
20	chr5:58818600-58818800	Enhancers	Stomach Mucosa	stomach
21	chr5:58818600-58820600	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr5:58818600-58821200	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr5:58818600-58821400	Weak transcription	HSMMtube	muscle

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