Variant report

Variant	rs17839658
Chromosome Location	chr5:127423013-127423014
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr5:127422938-127423026	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:127210281..127212908-chr5:127422377..127423931,2	MCF-7	breast:
2	chr5:127421756..127423811-chr5:127526808..127528561,2	K562	blood:
3	chr5:127301710..127304376-chr5:127421505..127423068,2	MCF-7	breast:
4	chr5:127422655..127424795-chr5:130496773..130499680,2	K562	blood:

Variant related genes	Relation type
ENSG00000245937	TF binding region
ENSG00000169567	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10089	1.00[YRI][hapmap]
rs10478797	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10519971	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13357283	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17164310	1.00[YRI][hapmap]
rs17164395	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805608	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3805610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3828656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56657382	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57249773	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72792276	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72792279	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72794361	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72794370	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72794379	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72794386	0.80[AFR][1000 genomes];0.94[ASN][1000 genomes]

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	esv1813981	chr5:127327649-127437401	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
2	nsv4993	chr5:127405214-127445622	Flanking Active TSS Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1812864	chr5:127408921-127427533	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:127416800-127424200	Active TSS	GM12878-XiMat	blood
2	chr5:127417000-127424200	Active TSS	Stomach Smooth Muscle	stomach
3	chr5:127417400-127423200	Active TSS	Brain Anterior Caudate	brain
4	chr5:127417400-127423400	Active TSS	Ovary	ovary
5	chr5:127417400-127423800	Active TSS	Fetal Intestine Large	intestine
6	chr5:127417400-127424400	Active TSS	Rectal Mucosa Donor 29	rectum
7	chr5:127420800-127424000	Active TSS	Fetal Intestine Small	intestine
8	chr5:127420800-127429600	Weak transcription	Aorta	Aorta
9	chr5:127421000-127423400	Enhancers	Fetal Heart	heart
10	chr5:127421000-127423600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr5:127421000-127423600	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr5:127421000-127423600	Active TSS	Fetal Stomach	stomach
13	chr5:127421000-127426400	Active TSS	Duodenum Mucosa	Duodenum
14	chr5:127421000-127426400	Weak transcription	Esophagus	oesophagus
15	chr5:127421000-127428200	Weak transcription	HSMM	muscle
16	chr5:127421000-127429600	Weak transcription	Gastric	stomach
17	chr5:127421000-127431600	Weak transcription	Primary T cells fromperipheralblood	blood
18	chr5:127421200-127423200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr5:127421200-127431400	Weak transcription	Fetal Muscle Trunk	muscle
20	chr5:127421400-127429400	Weak transcription	Primary B cells from peripheral blood	blood
21	chr5:127421400-127436400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr5:127421400-127450200	Weak transcription	Fetal Thymus	thymus
23	chr5:127421600-127423200	Enhancers	Primary B cells from cord blood	blood
24	chr5:127421600-127423600	Enhancers	Primary T helper cells PMA-I stimulated	--
25	chr5:127421600-127424800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:127421600-127426800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:127421600-127427000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr5:127421600-127427000	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr5:127421600-127429000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr5:127421600-127429800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
31	chr5:127421600-127432400	Weak transcription	Colon Smooth Muscle	Colon
32	chr5:127421600-127432400	Weak transcription	NHDF-Ad	bronchial
33	chr5:127421600-127432600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr5:127421600-127466800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr5:127421800-127426800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr5:127422000-127423600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr5:127422000-127433200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr5:127422000-127434200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:127422200-127423800	Enhancers	Dnd41	blood
40	chr5:127422200-127428800	Weak transcription	Primary hematopoietic stem cells	blood
41	chr5:127422400-127423200	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr5:127422400-127423600	Enhancers	Small Intestine	intestine
43	chr5:127422400-127426400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr5:127422400-127431400	Weak transcription	HMEC	breast
45	chr5:127422600-127423400	Enhancers	HUVEC	blood vessel
46	chr5:127422600-127423600	Active TSS	Rectal Smooth Muscle	rectum
47	chr5:127422600-127427000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr5:127422800-127423200	Flanking Active TSS	Brain Angular Gyrus	brain
49	chr5:127422800-127423200	Flanking Active TSS	Brain Substantia Nigra	brain
50	chr5:127422800-127423200	Weak transcription	Left Ventricle	heart

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