Variant report

Variant	rs4340879
Chromosome Location	chr5:179481302-179481303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:179477454..179480172-chr5:179480653..179484113,3	MCF-7	breast:
2	chr5:179480070..179481635-chr5:179485420..179487501,2	K562	blood:
3	chr5:179466250..179468313-chr5:179480534..179483405,2	MCF-7	breast:
4	chr5:179474557..179476078-chr5:179480075..179482538,2	MCF-7	breast:
5	chr5:179474524..179477374-chr5:179479073..179481485,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10051632	0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10061480	0.96[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10068039	0.82[CEU][hapmap]
rs10068529	0.96[CEU][hapmap];0.82[CHB][hapmap];0.81[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10068594	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10078977	0.96[CEU][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10464097	0.82[AFR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs10479455	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10479557	0.82[EUR][1000 genomes]
rs10903246	0.81[CEU][hapmap]
rs1102190	0.85[EUR][1000 genomes]
rs12153541	0.81[CEU][hapmap];0.83[CHB][hapmap];0.82[JPT][hapmap];0.84[EUR][1000 genomes]
rs12653944	0.81[CEU][hapmap]
rs13162328	0.82[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.94[YRI][hapmap];0.91[ASN][1000 genomes]
rs13176402	0.83[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1540526	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs173562	0.85[EUR][1000 genomes]
rs185076	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2083966	0.86[CHB][hapmap]
rs248257	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs248258	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs248316	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs248319	0.82[CEU][hapmap]
rs27013	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs27014	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs27016	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs27019	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs3749821	0.89[ASN][1000 genomes]
rs4130025	0.81[CEU][hapmap];0.83[CHB][hapmap];0.81[JPT][hapmap];0.84[EUR][1000 genomes]
rs418384	0.84[EUR][1000 genomes]
rs4466125	0.84[EUR][1000 genomes]
rs449511	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs4700858	0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.90[ASN][1000 genomes]
rs4700862	0.87[CHB][hapmap];0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs55734821	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs62405021	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6888883	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs723889	0.81[ASN][1000 genomes]
rs7706570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7734329	0.96[YRI][hapmap]
rs7734867	0.90[ASN][1000 genomes]
rs857182	0.85[EUR][1000 genomes]
rs857183	0.83[EUR][1000 genomes]
rs857189	0.85[EUR][1000 genomes]
rs9329096	0.96[CEU][hapmap];0.86[AMR][1000 genomes];0.95[EUR][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	nsv531997	chr5:179107599-179588082	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	339 gene(s)	inside rSNPs	diseases
2	nsv1030437	chr5:179235423-179649944	Enhancers Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
3	nsv537982	chr5:179235423-179649944	Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	189 gene(s)	inside rSNPs	diseases
4	nsv948909	chr5:179249099-179772640	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
5	nsv830561	chr5:179365637-179537012	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
6	nsv1033706	chr5:179402769-179806356	Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv1024592	chr5:179443133-179510642	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:179429800-179482600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr5:179461800-179483600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr5:179463800-179482200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
4	chr5:179464800-179483000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr5:179465400-179484200	Weak transcription	Aorta	Aorta
6	chr5:179467400-179483200	Weak transcription	HSMM	muscle
7	chr5:179472400-179496600	Weak transcription	Stomach Mucosa	stomach
8	chr5:179473200-179482000	Enhancers	Brain Substantia Nigra	brain
9	chr5:179473400-179481600	Enhancers	Brain Anterior Caudate	brain
10	chr5:179473800-179484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr5:179473800-179488000	Weak transcription	Fetal Stomach	stomach
12	chr5:179474000-179484000	Enhancers	Brain Cingulate Gyrus	brain
13	chr5:179474000-179496200	Weak transcription	Primary B cells from cord blood	blood
14	chr5:179475200-179481600	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr5:179475800-179483400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr5:179476000-179481600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr5:179476000-179484400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr5:179476000-179497800	Weak transcription	Lung	lung
19	chr5:179476400-179481400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
20	chr5:179476400-179486200	Weak transcription	Ovary	ovary
21	chr5:179476400-179487000	Weak transcription	Fetal Muscle Leg	muscle
22	chr5:179476400-179496800	Weak transcription	Right Ventricle	heart
23	chr5:179477400-179483800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr5:179477400-179494000	Weak transcription	Primary hematopoietic stem cells	blood
25	chr5:179477400-179495000	Weak transcription	Gastric	stomach
26	chr5:179477600-179483600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr5:179477600-179486200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr5:179477800-179481400	Weak transcription	HepG2	liver
29	chr5:179478000-179482400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:179478000-179496800	Weak transcription	Right Atrium	heart
31	chr5:179478400-179484200	Enhancers	Brain Hippocampus Middle	brain
32	chr5:179478600-179481400	Enhancers	Brain Germinal Matrix	brain
33	chr5:179478800-179493800	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr5:179479000-179481400	Enhancers	Colon Smooth Muscle	Colon
35	chr5:179479000-179481400	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr5:179479000-179481600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr5:179479000-179481600	Enhancers	Fetal Brain Female	brain
38	chr5:179479000-179482400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr5:179479400-179482000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr5:179479600-179481600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:179479600-179483400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
42	chr5:179479800-179496800	Weak transcription	Psoas Muscle	Psoas
43	chr5:179480000-179482600	Enhancers	iPS-20b Cell Line	embryonic stem cell
44	chr5:179480000-179483200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr5:179480000-179484000	Enhancers	HUES6 Cell Line	embryonic stem cell
46	chr5:179480000-179485400	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr5:179480200-179482200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr5:179480200-179486000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr5:179480200-179486800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr5:179480400-179481600	Weak transcription	Liver	Liver

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