Variant report

Variant	rs17797996
Chromosome Location	chr5:58843656-58843657
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:58832234..58834269-chr5:58843258..58845323,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1035321	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10491440	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491441	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs10491442	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514859	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950308	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11951110	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956402	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957151	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514190	1.00[ASN][1000 genomes]
rs12520633	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521279	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439074	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741863	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17798319	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081664	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41404047	0.83[CEU][hapmap]
rs56007967	1.00[ASN][1000 genomes]
rs62355561	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355562	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355581	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355582	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355584	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357524	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357525	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357527	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357530	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372240	1.00[ASN][1000 genomes]
rs72751212	1.00[ASN][1000 genomes]
rs72769726	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72769729	0.85[EUR][1000 genomes]
rs893190	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
4	nsv462189	chr5:58830145-58879822	Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
5	nsv598255	chr5:58830145-58879822	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58836600-58854400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:58836800-58857400	Weak transcription	Primary B cells from cord blood	blood
3	chr5:58840000-58851600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:58840200-58844600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr5:58840200-58849000	Weak transcription	Fetal Intestine Small	intestine
6	chr5:58840200-58849800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr5:58840200-58858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr5:58840400-58844200	Weak transcription	Liver	Liver
9	chr5:58840400-58850800	Weak transcription	Brain Substantia Nigra	brain
10	chr5:58840400-58853200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:58840400-58856200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:58840600-58844600	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr5:58840600-58844800	Weak transcription	Small Intestine	intestine
14	chr5:58840600-58851400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr5:58840800-58844600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr5:58840800-58858600	Weak transcription	Fetal Kidney	kidney
17	chr5:58841400-58844000	Weak transcription	Fetal Lung	lung
18	chr5:58842200-58844200	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr5:58842400-58845600	Enhancers	Stomach Mucosa	stomach
20	chr5:58843400-58843800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr5:58843400-58844000	Enhancers	Skeletal Muscle Male	skeletal muscle
22	chr5:58843400-58845200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr5:58843400-58845200	Enhancers	Hela-S3	cervix
24	chr5:58843600-58843800	Enhancers	Brain Hippocampus Middle	brain
25	chr5:58843600-58843800	Enhancers	Fetal Brain Male	brain
26	chr5:58843600-58844000	Enhancers	Brain Angular Gyrus	brain
27	chr5:58843600-58844000	Enhancers	Gastric	stomach
28	chr5:58843600-58844000	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr5:58843600-58844000	Transcr. at gene 5' and 3'	A549	lung
30	chr5:58843600-58845000	Enhancers	Psoas Muscle	Psoas
31	chr5:58843600-58845600	Enhancers	Colon Smooth Muscle	Colon

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