Variant report

Variant	rs17798319
Chromosome Location	chr5:58858708-58858709
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:58853948..58856765-chr5:58857609..58860199,2	MCF-7	breast:
2	chr5:58858064..58860308-chr5:58864549..58867326,2	K562	blood:
3	chr5:58853827..58855352-chr5:58858550..58860453,2	MCF-7	breast:

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1035321	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10491440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10491441	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10491442	1.00[CEU][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10514859	1.00[CEU][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11950308	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11951110	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11956402	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11957151	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12514190	1.00[ASN][1000 genomes]
rs12520633	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12521279	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17439074	0.86[CEU][hapmap];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17741863	1.00[CEU][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797996	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36081664	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56007967	1.00[ASN][1000 genomes]
rs62355561	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355562	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355581	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355582	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62355584	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357524	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357525	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357527	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62357530	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62372240	1.00[ASN][1000 genomes]
rs72751212	1.00[ASN][1000 genomes]
rs72769726	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72769729	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs893190	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs953302	0.85[AMR][1000 genomes];0.95[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:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:58840200-58858800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr5:58843800-58862400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr5:58850400-58860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:58851800-58859800	Weak transcription	Psoas Muscle	Psoas
5	chr5:58854000-58858800	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr5:58854600-58861600	Weak transcription	Fetal Brain Female	brain
7	chr5:58855600-58863000	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:58856600-58858800	Weak transcription	Brain Angular Gyrus	brain
9	chr5:58856600-58858800	Weak transcription	Brain Hippocampus Middle	brain
10	chr5:58856600-58858800	Weak transcription	Fetal Intestine Small	intestine
11	chr5:58856600-58864000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr5:58856600-58865400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr5:58856800-58858800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:58856800-58858800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr5:58856800-58859000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:58857200-58859200	Enhancers	Hela-S3	cervix
17	chr5:58857600-58859200	Enhancers	Primary hematopoietic stem cells	blood
18	chr5:58857800-58859600	Enhancers	iPS-15b Cell Line	embryonic stem cell
19	chr5:58857800-58859600	Enhancers	Muscle Satellite Cultured Cells	--
20	chr5:58857800-58859800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr5:58857800-58860200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr5:58857800-58860400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr5:58858000-58859800	Enhancers	HUES64 Cell Line	embryonic stem cell
24	chr5:58858200-58858800	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr5:58858200-58858800	Enhancers	GM12878-XiMat	blood
26	chr5:58858200-58859200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr5:58858200-58859400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr5:58858200-58859400	Enhancers	Fetal Intestine Large	intestine
29	chr5:58858200-58859400	Enhancers	NHEK	skin
30	chr5:58858200-58859600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr5:58858200-58859600	Enhancers	NH-A	brain
32	chr5:58858200-58860000	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr5:58858200-58860000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
34	chr5:58858200-58860200	Enhancers	Pancreatic Islets	Pancreatic Islet
35	chr5:58858200-58860400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr5:58858400-58859200	Enhancers	Primary B cells from cord blood	blood
37	chr5:58858400-58859400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:58858400-58859400	Enhancers	Brain Anterior Caudate	brain
39	chr5:58858400-58859600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr5:58858400-58859600	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr5:58858400-58859600	Flanking Active TSS	A549	lung
42	chr5:58858400-58859800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
43	chr5:58858400-58859800	Enhancers	iPS-18 Cell Line	embryonic stem cell
44	chr5:58858400-58859800	Enhancers	HepG2	liver
45	chr5:58858400-58859800	Enhancers	HSMM	muscle
46	chr5:58858400-58860000	Enhancers	HMEC	breast
47	chr5:58858600-58859000	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
48	chr5:58858600-58859000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
49	chr5:58858600-58859200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr5:58858600-58859200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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