Variant report

Variant	rs11743869
Chromosome Location	chr5:178301765-178301766
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:38619641..38620162-chr5:178301644..178302146,3	MCF-7	breast:
2	chr5:178299499..178302283-chr5:178303072..178304596,2	MCF-7	breast:
3	chr13:38619618..38620640-chr5:178301624..178302148,7	MCF-7	breast:

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10035887	0.88[EUR][1000 genomes]
rs10040956	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10067521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10077950	0.83[CHB][hapmap]
rs1046726	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10479515	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10479516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516151	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs11249603	0.85[EUR][1000 genomes]
rs11746382	0.84[EUR][1000 genomes]
rs11955586	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960446	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655480	0.83[CHB][hapmap]
rs12658098	0.83[CHB][hapmap]
rs13154558	0.87[EUR][1000 genomes]
rs1496949	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs1496950	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs17078820	0.81[JPT][hapmap]
rs17078829	0.81[JPT][hapmap]
rs1995079	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs4130052	1.00[CEU][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4700927	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs62393052	0.89[EUR][1000 genomes]
rs6600990	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6866021	0.88[EUR][1000 genomes]
rs6870709	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6872605	0.87[EUR][1000 genomes]
rs6872794	0.87[EUR][1000 genomes]
rs6873993	0.87[EUR][1000 genomes]
rs6877198	0.84[CHB][hapmap]
rs6885597	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6891035	0.84[CHB][hapmap]
rs7445694	0.83[CHB][hapmap]
rs7446225	0.83[CHB][hapmap]
rs7447547	0.83[CHB][hapmap]
rs7701607	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs7702579	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7702879	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs9329059	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[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	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

No data

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178287600-178302400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:178288200-178317400	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
3	chr5:178288800-178302200	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr5:178288800-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr5:178289400-178302200	Strong transcription	Brain Anterior Caudate	brain
6	chr5:178289600-178317400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:178290000-178302200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:178291200-178317400	ZNF genes & repeats	Liver	Liver
9	chr5:178292000-178303000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
10	chr5:178292200-178302200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
11	chr5:178292600-178305000	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:178292600-178305200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr5:178296000-178305000	ZNF genes & repeats	A549	lung
14	chr5:178296000-178305200	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr5:178296000-178305400	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
16	chr5:178296000-178319200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
17	chr5:178296200-178315600	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
18	chr5:178296200-178319200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:178296400-178302400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr5:178296400-178311200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
21	chr5:178296400-178317600	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
22	chr5:178297200-178315800	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
23	chr5:178297400-178315600	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
24	chr5:178297400-178317400	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr5:178297400-178317400	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
26	chr5:178297400-178317400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:178297600-178303600	ZNF genes & repeats	NHEK	skin
28	chr5:178297600-178305000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr5:178297600-178305200	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
30	chr5:178297600-178317400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr5:178298000-178305200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
32	chr5:178298200-178302000	Weak transcription	Placenta Amnion	Placenta Amnion
33	chr5:178298200-178305000	Strong transcription	Psoas Muscle	Psoas
34	chr5:178298400-178301800	Strong transcription	HSMM	muscle
35	chr5:178298400-178305000	ZNF genes & repeats	Brain Substantia Nigra	brain
36	chr5:178298600-178302000	Strong transcription	Placenta	Placenta
37	chr5:178298600-178302200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr5:178298600-178304000	Strong transcription	Fetal Kidney	kidney
39	chr5:178298600-178305000	ZNF genes & repeats	Brain Hippocampus Middle	brain
40	chr5:178298800-178302000	Weak transcription	Right Ventricle	heart
41	chr5:178298800-178317800	ZNF genes & repeats	Primary T cells from cord blood	blood
42	chr5:178299000-178303400	ZNF genes & repeats	HMEC	breast
43	chr5:178299000-178310600	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
44	chr5:178299000-178317600	ZNF genes & repeats	Fetal Brain Female	brain
45	chr5:178299200-178314000	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
46	chr5:178299400-178303000	Strong transcription	Fetal Heart	heart
47	chr5:178299400-178305000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
48	chr5:178299400-178310200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
49	chr5:178299400-178317400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr5:178299600-178302200	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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