Variant report

Variant	rs11128930
Chromosome Location	chr3:20022050-20022051
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:19988550..19992168-chr3:20020469..20024167,3	K562	blood:
2	chr3:19988069..19990118-chr3:20020900..20023827,2	MCF-7	breast:
3	chr3:19998852..20001425-chr3:20020103..20022422,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs11128927	0.90[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11128928	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11128929	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];0.91[JPT][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1143451	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12631435	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13065319	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13068289	0.83[EUR][1000 genomes]
rs13070718	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13072891	0.90[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs13076973	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13077307	0.84[ASN][1000 genomes]
rs13078505	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13082980	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13086159	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13089853	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13093485	0.83[EUR][1000 genomes]
rs13097697	0.95[EUR][1000 genomes]
rs13098388	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17181400	0.94[CEU][hapmap];0.90[CHB][hapmap];0.96[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17181862	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17796115	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34305656	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34343204	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34417128	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34705953	0.87[ASN][1000 genomes]
rs34872212	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35175665	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35482904	0.88[ASN][1000 genomes]
rs35684714	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35713165	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4610240	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs58859849	0.82[ASN][1000 genomes]
rs59086970	0.86[ASN][1000 genomes]
rs59608170	0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60255931	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6796425	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71316239	0.95[EUR][1000 genomes]
rs7434271	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7614695	0.91[ASN][1000 genomes]
rs7615145	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7618928	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633940	0.91[ASN][1000 genomes]
rs7634934	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643167	0.81[EUR][1000 genomes]
rs7646128	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9877801	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9878879	0.92[EUR][1000 genomes];0.96[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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	nsv997486	chr3:20006702-20113989	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
12	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11128930	EFHB	cis	normal skin	skin_eQTL
rs11128930	EFHB	cis	cerebellum	SCAN
rs11128930	EFHB	cis	Skin Sun Exposed Lower leg	GTEx
rs11128930	EFHB	cis	multi-tissue	Pritchard
rs11128930	EFHB	cis	parietal	SCAN
rs11128930	EFHB	cis	Artery Tibial	GTEx
rs11128930	EFHB	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:19993600-20023600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr3:19993800-20023800	Weak transcription	Small Intestine	intestine
3	chr3:19997800-20023200	Weak transcription	Spleen	Spleen
4	chr3:19999600-20027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr3:20003800-20023600	Weak transcription	Aorta	Aorta
6	chr3:20008800-20035600	Weak transcription	Psoas Muscle	Psoas
7	chr3:20011800-20026400	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr3:20011800-20027400	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:20011800-20028000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:20012000-20027800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr3:20012000-20027800	Strong transcription	Primary T helper cells fromperipheralblood	blood
12	chr3:20012200-20023600	Weak transcription	Brain Angular Gyrus	brain
13	chr3:20012200-20023600	Weak transcription	Gastric	stomach
14	chr3:20012200-20025600	Weak transcription	Pancreas	Pancrea
15	chr3:20012200-20026400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr3:20012400-20025600	Weak transcription	Stomach Mucosa	stomach
17	chr3:20012400-20027600	Strong transcription	Primary B cells from cord blood	blood
18	chr3:20012400-20033600	Weak transcription	Fetal Brain Male	brain
19	chr3:20012600-20023200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr3:20013400-20022200	Weak transcription	Lung	lung
21	chr3:20013800-20023800	Weak transcription	Right Ventricle	heart
22	chr3:20014400-20025600	Strong transcription	K562	blood
23	chr3:20014400-20027000	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:20014600-20026400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr3:20014600-20027600	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr3:20015200-20025200	Weak transcription	Pancreatic Islets	Pancreatic Islet
27	chr3:20015200-20026800	Strong transcription	Rectal Mucosa Donor 29	rectum
28	chr3:20015200-20027000	Strong transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:20015200-20027200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr3:20015200-20027600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:20015200-20027600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr3:20015200-20030000	Strong transcription	Fetal Thymus	thymus
33	chr3:20015400-20025000	Strong transcription	Fetal Muscle Trunk	muscle
34	chr3:20015400-20025200	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr3:20015400-20025400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr3:20015400-20025400	Strong transcription	GM12878-XiMat	blood
37	chr3:20015400-20025800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:20015400-20027200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr3:20015400-20027400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr3:20015400-20027600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:20015400-20028200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:20015400-20028200	Strong transcription	Placenta	Placenta
43	chr3:20015600-20024400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr3:20015600-20025400	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr3:20015600-20025400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr3:20015600-20025600	Strong transcription	Fetal Lung	lung
47	chr3:20015600-20025800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:20015600-20026200	Strong transcription	Fetal Muscle Leg	muscle
49	chr3:20015600-20026400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr3:20015600-20026600	Strong transcription	Primary T cells fromperipheralblood	blood

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