Variant report

Variant	rs11960161
Chromosome Location	chr5:178453837-178453838
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:178450308..178453089-chr5:178453235..178455700,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000234284	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10479519	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10479520	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10516149	1.00[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10516150	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505147	0.82[ASN][1000 genomes]
rs11951738	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958355	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152869	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160086	0.86[ASN][1000 genomes]
rs13161528	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188724	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13359549	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359570	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359572	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361077	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17078988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132671	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132672	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054398	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431447	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34881171	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35568336	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797615	1.00[CHB][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]
rs4700780	1.00[CHB][hapmap];0.81[JPT][hapmap];0.94[ASN][1000 genomes]
rs4700781	0.88[ASN][1000 genomes]
rs4701030	1.00[CHB][hapmap];0.90[JPT][hapmap];0.95[ASN][1000 genomes]
rs4701045	0.88[ASN][1000 genomes]
rs58827878	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60061283	0.90[ASN][1000 genomes]
rs60073676	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62393072	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393074	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393075	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62393076	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601007	1.00[CEU][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601010	0.86[CHB][hapmap];0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs6859576	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859767	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860309	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861539	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867119	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867208	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868893	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875473	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875622	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880315	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888539	0.90[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6888567	0.89[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6890317	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6891216	1.00[JPT][hapmap]
rs7707587	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708743	0.92[ASN][1000 genomes]
rs7709054	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711420	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732719	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv883221	chr5:178410538-178454118	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking 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	5 gene(s)	inside rSNPs	diseases
10	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11960161	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL
rs11960161	DKFZp686E2433	cis	Lymphoblastoid	GTEx

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178451200-178461800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
2	chr5:178451400-178458000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr5:178451400-178461800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr5:178451600-178454000	Weak transcription	HSMM	muscle
5	chr5:178451600-178456000	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr5:178451600-178456000	ZNF genes & repeats	Fetal Intestine Small	intestine
7	chr5:178451600-178460600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr5:178451600-178461400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr5:178451600-178461800	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
10	chr5:178451800-178454000	Weak transcription	NHLF	lung
11	chr5:178451800-178454000	Weak transcription	Osteobl	bone
12	chr5:178451800-178456000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
13	chr5:178451800-178456000	ZNF genes & repeats	Fetal Intestine Large	intestine
14	chr5:178451800-178457800	Weak transcription	HUVEC	blood vessel
15	chr5:178451800-178460800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr5:178451800-178461800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr5:178451800-178461800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:178451800-178464000	ZNF genes & repeats	Liver	Liver
19	chr5:178452000-178454000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr5:178452000-178454000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr5:178452000-178454000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr5:178452000-178454000	Weak transcription	Psoas Muscle	Psoas
23	chr5:178452000-178454000	Weak transcription	HepG2	liver
24	chr5:178452000-178454000	Weak transcription	NHDF-Ad	bronchial
25	chr5:178452000-178455000	Weak transcription	Muscle Satellite Cultured Cells	--
26	chr5:178452000-178456200	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
27	chr5:178452200-178454000	Weak transcription	Fetal Brain Male	brain
28	chr5:178452200-178454000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:178452400-178454000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr5:178452400-178454000	Weak transcription	Brain Cingulate Gyrus	brain
31	chr5:178452400-178455200	Strong transcription	Fetal Muscle Trunk	muscle
32	chr5:178452600-178454200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr5:178452800-178454400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
34	chr5:178453000-178454000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr5:178453000-178456000	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
36	chr5:178453000-178456400	ZNF genes & repeats	Fetal Muscle Leg	muscle
37	chr5:178453000-178461000	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
38	chr5:178453000-178461000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
39	chr5:178453000-178461800	ZNF genes & repeats	Brain Anterior Caudate	brain
40	chr5:178453000-178464000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
41	chr5:178453200-178454400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr5:178453200-178455000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr5:178453200-178460800	ZNF genes & repeats	Primary B cells from peripheral blood	blood
44	chr5:178453200-178460800	ZNF genes & repeats	Primary T cells from cord blood	blood
45	chr5:178453200-178461000	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
46	chr5:178453200-178461200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
47	chr5:178453200-178461200	ZNF genes & repeats	Fetal Kidney	kidney
48	chr5:178453200-178461800	ZNF genes & repeats	Primary hematopoietic stem cells	blood
49	chr5:178453200-178461800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
50	chr5:178453200-178461800	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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