Variant report

Variant	rs11747390
Chromosome Location	chr5:178155304-178155305
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178154802..178159439-chr5:178284936..178288781,7	MCF-7	breast:
2	chr5:178152146..178155385-chr5:178293103..178294784,3	MCF-7	breast:
3	chr5:178154460..178156007-chr5:178156141..178157886,2	MCF-7	breast:
4	chr5:178152814..178155589-chr5:178155933..178157780,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178338	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10043035	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1071881	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1071882	0.83[CEU][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1071883	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[LWK][hapmap];0.97[TSI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1079487	0.86[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11249566	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1132336	0.87[ASW][hapmap];0.83[CEU][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11740283	0.83[CEU][hapmap];0.84[LWK][hapmap];0.97[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11742156	0.83[CEU][hapmap];0.97[TSI][hapmap];0.87[EUR][1000 genomes]
rs11742176	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11743893	0.85[TSI][hapmap]
rs11747097	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11747232	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750409	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11750784	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13167549	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13173130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13186580	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34601045	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34645905	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34651317	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34703961	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34981407	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35007468	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35287913	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35528027	0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs35579651	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs35850587	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4266420	1.00[ASW][hapmap];0.83[CEU][hapmap];0.86[LWK][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4470778	1.00[ASW][hapmap];0.88[TSI][hapmap]
rs4533908	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4612090	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs55774261	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55818572	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55912234	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs55974982	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56027952	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56070635	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56236920	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56328282	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs59259518	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62392839	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62392842	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62392851	0.84[AMR][1000 genomes]
rs62392852	0.92[ASN][1000 genomes]
rs62392853	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs62392854	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66947564	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6870021	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6890741	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6896799	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71611460	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[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	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
4	nsv1031206	chr5:178149292-178283614	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
5	nsv537973	chr5:178149292-178283614	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11747390	FAM193B	cis	parietal	SCAN
rs11747390	ZNF354A	cis	Thyroid	GTEx
rs11747390	ZNF354A	cis	lymphoblastoid	seeQTL
rs11747390	ZNF354A	cis	cerebellum	SCAN

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178135800-178155600	ZNF genes & repeats	Liver	Liver
2	chr5:178138400-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr5:178138800-178155600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr5:178140600-178156600	Weak transcription	Hela-S3	cervix
5	chr5:178140800-178156000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
6	chr5:178141800-178155600	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr5:178142800-178155600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:178144600-178155600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr5:178145400-178155400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
10	chr5:178147800-178155400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr5:178148000-178155400	Strong transcription	Fetal Muscle Trunk	muscle
12	chr5:178148000-178155600	Strong transcription	HUES64 Cell Line	embryonic stem cell
13	chr5:178148000-178155600	Strong transcription	Right Ventricle	heart
14	chr5:178148400-178156600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr5:178148800-178155600	Strong transcription	HUES6 Cell Line	embryonic stem cell
16	chr5:178149200-178156400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr5:178149400-178155400	Strong transcription	Skeletal Muscle Female	skeletal muscle
18	chr5:178149400-178156600	Weak transcription	Stomach Mucosa	stomach
19	chr5:178149400-178164400	Weak transcription	Fetal Heart	heart
20	chr5:178149600-178156400	Weak transcription	HSMM	muscle
21	chr5:178149800-178155400	Strong transcription	HUES48 Cell Line	embryonic stem cell
22	chr5:178149800-178155400	Strong transcription	Primary T helper cells fromperipheralblood	blood
23	chr5:178149800-178157000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr5:178150000-178156800	Weak transcription	HUVEC	blood vessel
25	chr5:178150400-178155400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr5:178150400-178156600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr5:178150600-178155400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr5:178150600-178156200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr5:178150600-178156600	Weak transcription	NHLF	lung
30	chr5:178150800-178156800	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr5:178151000-178155400	Strong transcription	Brain Substantia Nigra	brain
32	chr5:178151200-178155600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr5:178151400-178155400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr5:178151400-178155400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr5:178151400-178155400	ZNF genes & repeats	Fetal Brain Female	brain
36	chr5:178151400-178155400	Strong transcription	Fetal Muscle Leg	muscle
37	chr5:178151400-178155400	Strong transcription	Skeletal Muscle Male	skeletal muscle
38	chr5:178151400-178155600	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr5:178152000-178155400	ZNF genes & repeats	Primary B cells from cord blood	blood
40	chr5:178152000-178155600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr5:178152200-178155400	ZNF genes & repeats	A549	lung
42	chr5:178152600-178155400	Strong transcription	Brain Hippocampus Middle	brain
43	chr5:178152600-178156400	Weak transcription	NHDF-Ad	bronchial
44	chr5:178152800-178155400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
45	chr5:178152800-178155400	Strong transcription	Duodenum Smooth Muscle	Duodenum
46	chr5:178152800-178156400	Weak transcription	Fetal Brain Male	brain
47	chr5:178152800-178157200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr5:178153200-178155400	Strong transcription	Muscle Satellite Cultured Cells	--
49	chr5:178153200-178156000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr5:178153200-178156400	Weak transcription	Colonic Mucosa	Colon

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