Variant report

Variant	rs11128929
Chromosome Location	chr3:19996373-19996374
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:19987480..19989660-chr3:19996323..19998191,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11128927	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11128928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11128930	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11128931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1143451	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12629485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12631435	0.82[EUR][1000 genomes]
rs13065319	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13068289	0.81[EUR][1000 genomes]
rs13070718	0.83[EUR][1000 genomes]
rs13072891	0.90[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs13076973	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077307	0.89[ASN][1000 genomes]
rs13078505	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13082980	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13086159	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13089853	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13093485	0.81[EUR][1000 genomes]
rs13097697	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13098388	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17181400	0.94[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17181862	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17796115	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34305656	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34343204	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34417128	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34705953	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34872212	0.81[EUR][1000 genomes]
rs35175665	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35482904	0.83[ASN][1000 genomes]
rs35684714	0.81[EUR][1000 genomes]
rs35713165	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4610240	0.94[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs58859849	0.87[ASN][1000 genomes]
rs59086970	0.91[ASN][1000 genomes]
rs59608170	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60255931	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6796425	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs71316239	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7434271	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7614695	0.86[ASN][1000 genomes]
rs7615145	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618928	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7633940	0.86[ASN][1000 genomes]
rs7634934	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7646128	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877801	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9878879	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv433358	chr3:19547184-19996508	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	esv1828161	chr3:19547184-20062060	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	esv1825914	chr3:19549859-20137270	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
4	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
5	esv1826570	chr3:19579860-20077414	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
6	esv1833139	chr3:19579860-20121349	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	esv1826254	chr3:19592688-20042834	Flanking Active TSS Strong transcription Weak transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
8	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
10	esv1825988	chr3:19976375-20102773	Flanking Active TSS Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
11	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11128929	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs11128929	EFHB	cis	normal skin	skin_eQTL
rs11128929	EFHB	cis	Muscle Skeletal	GTEx
rs11128929	EFHB	cis	Artery Tibial	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19989800-20018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr3:19990000-20008600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:19990000-20016200	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr3:19990800-19996600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:19990800-20017000	Weak transcription	Fetal Kidney	kidney
6	chr3:19991000-19996600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:19991000-20001800	Weak transcription	Brain Angular Gyrus	brain
8	chr3:19991200-20002600	Weak transcription	Fetal Heart	heart
9	chr3:19991400-19998200	Weak transcription	Aorta	Aorta
10	chr3:19991400-19998800	Strong transcription	Fetal Thymus	thymus
11	chr3:19991400-20017000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:19991600-19997200	Strong transcription	NH-A	brain
13	chr3:19991600-19998400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:19991600-19998400	Weak transcription	Psoas Muscle	Psoas
15	chr3:19991600-20003800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:19991600-20003800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr3:19991800-19997600	Strong transcription	Primary B cells from peripheral blood	blood
18	chr3:19991800-19998000	Strong transcription	Fetal Intestine Large	intestine
19	chr3:19992000-19998200	Strong transcription	K562	blood
20	chr3:19992000-20000000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:19992000-20000200	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr3:19992000-20000400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr3:19992000-20003400	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:19992000-20004000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:19992200-19996600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr3:19992200-19998400	Strong transcription	Placenta	Placenta
27	chr3:19992200-20001000	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr3:19992200-20012200	Weak transcription	Stomach Mucosa	stomach
29	chr3:19992400-19997000	Strong transcription	H1 Cell Line	embryonic stem cell
30	chr3:19992400-19997400	Strong transcription	Sigmoid Colon	Sigmoid Colon
31	chr3:19992400-19997600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr3:19992400-19997600	Strong transcription	Rectal Mucosa Donor 29	rectum
33	chr3:19992400-19997800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr3:19992400-19997800	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr3:19992400-19998200	Strong transcription	Osteobl	bone
36	chr3:19992400-19998400	Strong transcription	Duodenum Mucosa	Duodenum
37	chr3:19992400-19998600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:19992400-19999000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr3:19992400-20001000	Strong transcription	HUES6 Cell Line	embryonic stem cell
40	chr3:19992600-19998400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:19992600-20000400	Strong transcription	HSMM	muscle
42	chr3:19992600-20003800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
43	chr3:19992800-19998800	Strong transcription	Cortex derived primary cultured neurospheres	brain
44	chr3:19992800-19999000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:19993000-19996400	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr3:19993000-19997800	Strong transcription	Brain Anterior Caudate	brain
47	chr3:19993000-19997800	Strong transcription	Rectal Mucosa Donor 31	rectum
48	chr3:19993200-19998800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:19993200-19999600	Strong transcription	Primary B cells from cord blood	blood
50	chr3:19993200-20000200	Strong transcription	Muscle Satellite Cultured Cells	--

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