Variant report

Variant	rs11740486
Chromosome Location	chr5:178288983-178288984
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:178285646..178289279-chr5:178321547..178324884,4	MCF-7	breast:
2	chr5:177640785..177642286-chr5:178288319..178291268,2	K562	blood:
3	chr5:178156014..178158845-chr5:178285994..178289826,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000198939	Chromatin interaction
ENSG00000169131	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1046724	0.83[EUR][1000 genomes]
rs11249600	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11740503	1.00[ASN][1000 genomes]
rs11744810	0.83[EUR][1000 genomes]
rs11745435	0.83[EUR][1000 genomes]
rs11748636	0.83[EUR][1000 genomes]
rs11749871	0.82[EUR][1000 genomes]
rs11955491	0.82[EUR][1000 genomes]
rs11956161	0.83[EUR][1000 genomes]
rs13166562	0.80[ASN][1000 genomes]
rs2047356	0.82[EUR][1000 genomes]
rs34904538	0.83[EUR][1000 genomes]
rs35245718	0.81[EUR][1000 genomes]
rs35974815	0.83[EUR][1000 genomes]
rs35984063	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36077478	0.91[ASN][1000 genomes]
rs6894647	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7445002	0.83[EUR][1000 genomes]
rs7448421	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7448445	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7722159	0.80[ASN][1000 genomes]
rs7722441	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883218	chr5:178219855-178349391	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	nsv462574	chr5:178269682-178313078	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv600463	chr5:178269682-178313078	Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv823352	chr5:178279625-178296623	Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178289600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr5:178287600-178289600	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr5:178287600-178289600	Weak transcription	Right Atrium	heart
4	chr5:178287600-178289800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr5:178287600-178289800	Weak transcription	Fetal Thymus	thymus
6	chr5:178287600-178291000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr5:178287600-178292000	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:178287600-178292200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
9	chr5:178287600-178292400	Weak transcription	Aorta	Aorta
10	chr5:178287600-178292600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr5:178287600-178294000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr5:178287600-178296200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
14	chr5:178287800-178289200	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr5:178287800-178289600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr5:178287800-178289600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr5:178287800-178289800	Weak transcription	HUES48 Cell Line	embryonic stem cell
18	chr5:178287800-178293200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr5:178288000-178289600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr5:178288200-178289000	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr5:178288200-178289000	Enhancers	Primary T cells fromperipheralblood	blood
22	chr5:178288200-178289000	Enhancers	Fetal Brain Male	brain
23	chr5:178288200-178289000	Genic enhancers	Fetal Muscle Leg	muscle
24	chr5:178288200-178289200	Enhancers	Left Ventricle	heart
25	chr5:178288200-178290200	Genic enhancers	K562	blood
26	chr5:178288200-178295000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr5:178288400-178289000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr5:178288400-178289000	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr5:178288400-178289000	Transcr. at gene 5' and 3'	Brain Germinal Matrix	brain
31	chr5:178288400-178289000	Enhancers	Brain Substantia Nigra	brain
32	chr5:178288400-178289000	Enhancers	Fetal Heart	heart
33	chr5:178288400-178289000	Genic enhancers	Fetal Kidney	kidney
34	chr5:178288400-178289000	Genic enhancers	Fetal Stomach	stomach
35	chr5:178288400-178289000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr5:178288400-178289000	Enhancers	Small Intestine	intestine
37	chr5:178288400-178289000	Enhancers	Stomach Mucosa	stomach
38	chr5:178288400-178289200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr5:178288400-178289200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr5:178288400-178289200	Flanking Active TSS	Placenta	Placenta
41	chr5:178288400-178289400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:178288400-178289400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
43	chr5:178288400-178289600	Enhancers	Lung	lung
44	chr5:178288400-178289800	Enhancers	Primary T helper naive cells from peripheral blood	blood
45	chr5:178288400-178290000	ZNF genes & repeats	Liver	Liver
46	chr5:178288400-178290000	Genic enhancers	Brain Inferior Temporal Lobe	brain
47	chr5:178288400-178290000	Genic enhancers	Ovary	ovary
48	chr5:178288400-178290200	Transcr. at gene 5' and 3'	Dnd41	blood
49	chr5:178288400-178290600	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr5:178288400-178290600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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