Variant report

Variant	rs6896799
Chromosome Location	chr5:178147014-178147015
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178140402..178144156-chr5:178146582..178150587,3	MCF-7	breast:
2	chr5:178135058..178137507-chr5:178144599..178147677,3	MCF-7	breast:
3	chr5:178145453..178147162-chr5:178151776..178154712,2	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10043035	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1071881	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1071882	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1071883	1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1079487	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1132336	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1132338	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11739893	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11740283	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11742156	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11742176	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11742808	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11743893	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11747097	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11747232	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11747390	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11748495	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11748497	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11749438	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11750409	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13173130	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13186580	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17184281	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17184302	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17184344	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17652247	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34601045	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34651317	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34703961	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34981407	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs35007468	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs35850587	0.88[EUR][1000 genomes]
rs4266420	1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4470778	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55774261	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55818572	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55974982	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56027952	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs56070635	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56159071	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56206101	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56236920	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58549512	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59259518	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61247551	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62392825	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62392826	0.83[ASN][1000 genomes]
rs62392827	0.85[ASN][1000 genomes]
rs62392831	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392832	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392833	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62392839	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62392842	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62392854	0.83[EUR][1000 genomes]
rs66947564	0.84[EUR][1000 genomes]
rs6870021	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6873150	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6890741	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71611460	0.81[EUR][1000 genomes]
rs72812613	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7732764	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[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	nsv948342	chr5:177384542-178168737	Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	141 gene(s)	inside rSNPs	diseases
2	nsv1031666	chr5:177988601-178236068	Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv883217	chr5:178099758-178193081	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6896799	ZNF354A	cis	Whole Blood	GTEx
rs6896799	ZNF354A	cis	Thyroid	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178130000-178150600	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr5:178135400-178150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr5:178135800-178147600	ZNF genes & repeats	Skeletal Muscle Male	skeletal muscle
4	chr5:178135800-178155600	ZNF genes & repeats	Liver	Liver
5	chr5:178136200-178155200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
6	chr5:178136800-178150400	ZNF genes & repeats	Brain Substantia Nigra	brain
7	chr5:178136800-178150600	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr5:178136800-178152800	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
9	chr5:178137000-178149800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
10	chr5:178137000-178150600	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
11	chr5:178137000-178150600	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
12	chr5:178137200-178151000	ZNF genes & repeats	Fetal Brain Female	brain
13	chr5:178137400-178147800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr5:178137400-178150600	ZNF genes & repeats	Psoas Muscle	Psoas
15	chr5:178138400-178149800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:178138400-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr5:178138600-178147600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
18	chr5:178138600-178147600	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
19	chr5:178138600-178147600	ZNF genes & repeats	Osteobl	bone
20	chr5:178138600-178148000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
21	chr5:178138600-178148800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
22	chr5:178138600-178149400	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
23	chr5:178138600-178149600	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
24	chr5:178138600-178150400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr5:178138600-178150600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr5:178138600-178150600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr5:178138600-178150600	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:178138800-178150200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr5:178138800-178150400	ZNF genes & repeats	Primary B cells from cord blood	blood
30	chr5:178138800-178154400	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
31	chr5:178138800-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr5:178139000-178149600	ZNF genes & repeats	Fetal Lung	lung
33	chr5:178139000-178150600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
34	chr5:178139000-178150600	ZNF genes & repeats	NHEK	skin
35	chr5:178139000-178154000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
36	chr5:178139200-178149000	ZNF genes & repeats	NH-A	brain
37	chr5:178139200-178150600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr5:178139200-178150600	ZNF genes & repeats	Left Ventricle	heart
39	chr5:178139200-178150600	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
40	chr5:178139200-178150600	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
41	chr5:178139200-178150800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
42	chr5:178139400-178154800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr5:178139600-178149200	ZNF genes & repeats	Primary T cells from cord blood	blood
44	chr5:178139600-178149800	ZNF genes & repeats	Stomach Smooth Muscle	stomach
45	chr5:178139600-178152800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
46	chr5:178139800-178147600	ZNF genes & repeats	HMEC	breast
47	chr5:178139800-178148000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr5:178139800-178148000	ZNF genes & repeats	Fetal Muscle Trunk	muscle
49	chr5:178139800-178149000	ZNF genes & repeats	Fetal Muscle Leg	muscle
50	chr5:178139800-178149800	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell

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