Variant report

Variant	rs10838732
Chromosome Location	chr11:47607940-47607941
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr11:47606467-47608044	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr11:47607176-47608004	K562	blood:	n/a	n/a
3	POLR2A	chr11:47606438-47608201	K562	blood:	n/a	n/a
4	POLR2A	chr11:47607700-47607946	GM12878	blood:	n/a	n/a
5	POLR2A	chr11:47607838-47608002	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:47587234..47588763-chr11:47607056..47608888,2	MCF-7	breast:

Variant related genes	Relation type
FAM180B	TF binding region
ENSG00000110536	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs1056387	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes]
rs10742814	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs10742817	1.00[CEU][hapmap];0.94[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs10742820	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs10769264	0.95[JPT][hapmap]
rs10769285	0.87[AMR][1000 genomes]
rs10769288	0.85[CEU][hapmap];0.89[CHB][hapmap]
rs10838709	0.95[JPT][hapmap]
rs10838726	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs10838731	0.85[ASN][1000 genomes]
rs10838736	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10838739	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10838740	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs10838741	0.87[AMR][1000 genomes]
rs10838745	0.81[AMR][1000 genomes]
rs10838746	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs10838758	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10838759	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs10838760	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs11039225	0.95[JPT][hapmap]
rs11039244	0.90[JPT][hapmap]
rs11039280	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AMR][1000 genomes]
rs11039290	0.82[ASN][1000 genomes]
rs11039297	0.82[ASN][1000 genomes]
rs11039329	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs11039332	0.90[JPT][hapmap]
rs11039336	0.82[AMR][1000 genomes]
rs11039337	0.87[AMR][1000 genomes]
rs11039345	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes]
rs11039373	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs11039377	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs12226431	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs12226590	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12285933	1.00[YRI][hapmap]
rs12286721	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs12292911	0.95[JPT][hapmap]
rs12362318	0.82[AMR][1000 genomes]
rs12785949	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap]
rs1563821	1.00[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs2203712	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]
rs2242081	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2290851	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2293576	0.95[JPT][hapmap]
rs3740699	1.00[CEU][hapmap];0.89[JPT][hapmap];0.85[YRI][hapmap]
rs3758655	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes]
rs4539273	0.96[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap]
rs4752858	0.80[ASN][1000 genomes]
rs4752860	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap]
rs4752865	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs6485758	0.95[JPT][hapmap]
rs6485763	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6485773	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs6485775	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7103648	0.95[JPT][hapmap]
rs7105791	0.86[AMR][1000 genomes]
rs7107792	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7107922	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7108479	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7114813	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7116970	0.85[AMR][1000 genomes]
rs7120548	0.95[JPT][hapmap]
rs7126378	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7129797	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs71475921	0.82[ASN][1000 genomes]
rs7927445	0.90[JPT][hapmap]
rs7929014	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7932703	1.00[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7933019	0.95[JPT][hapmap]
rs7933184	0.87[AMR][1000 genomes]
rs7935344	0.82[AMR][1000 genomes]
rs7935521	0.82[AMR][1000 genomes]
rs7935528	0.85[AMR][1000 genomes]
rs7936948	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes]
rs7939420	0.96[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap]
rs7943213	0.87[AMR][1000 genomes]
rs7945312	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7950696	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832142	chr11:47517955-47681310	Weak transcription Genic enhancers Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv825872	chr11:47565425-47660330	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10838732		cis	Lymphoblastoid	GTEx
rs10838732	C1QTNF4	cis	multi-tissue	Pritchard
rs10838732	FNBP4	Cis_1M	lymphoblastoid	RTeQTL
rs10838732	FNBP4	cis	lesional skin	skin_eQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47601400-47611800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr11:47601400-47613400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr11:47602000-47608000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
4	chr11:47602000-47608200	Strong transcription	Placenta	Placenta
5	chr11:47602200-47608200	Strong transcription	Primary B cells from peripheral blood	blood
6	chr11:47602200-47608200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr11:47602200-47608800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr11:47602200-47610400	Strong transcription	Fetal Brain Female	brain
9	chr11:47602400-47608000	Strong transcription	Sigmoid Colon	Sigmoid Colon
10	chr11:47602400-47608200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr11:47602400-47608200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr11:47602400-47608400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr11:47602400-47609000	Strong transcription	Fetal Intestine Small	intestine
14	chr11:47602400-47609200	Strong transcription	Primary B cells from cord blood	blood
15	chr11:47602400-47609800	Strong transcription	Fetal Stomach	stomach
16	chr11:47602600-47608000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr11:47602600-47608800	Strong transcription	Thymus	Thymus
18	chr11:47602600-47610000	Strong transcription	Brain Germinal Matrix	brain
19	chr11:47603000-47608600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:47603800-47612400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr11:47604000-47608800	Weak transcription	Stomach Mucosa	stomach
22	chr11:47604000-47612000	Weak transcription	Small Intestine	intestine
23	chr11:47604400-47610800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr11:47605000-47611000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr11:47605600-47610800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr11:47605800-47608200	Weak transcription	NHDF-Ad	bronchial
27	chr11:47605800-47608400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr11:47605800-47608800	Weak transcription	Fetal Brain Male	brain
29	chr11:47605800-47610200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr11:47605800-47610200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr11:47605800-47610200	Weak transcription	Fetal Kidney	kidney
32	chr11:47605800-47610800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr11:47606000-47608000	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr11:47606000-47609200	Weak transcription	HSMM	muscle
35	chr11:47606000-47610400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:47606000-47611000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
37	chr11:47606000-47611400	Weak transcription	HMEC	breast
38	chr11:47606000-47614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr11:47606200-47608000	Weak transcription	Brain Angular Gyrus	brain
40	chr11:47606200-47608400	Weak transcription	Aorta	Aorta
41	chr11:47606200-47608800	Weak transcription	Hela-S3	cervix
42	chr11:47606200-47609200	Weak transcription	K562	blood
43	chr11:47606200-47609200	Weak transcription	NHLF	lung
44	chr11:47606200-47609400	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr11:47606200-47610200	Weak transcription	Colon Smooth Muscle	Colon
46	chr11:47606200-47610800	Weak transcription	Fetal Heart	heart
47	chr11:47606200-47610800	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr11:47606200-47611200	Weak transcription	Colonic Mucosa	Colon
49	chr11:47606200-47611400	Weak transcription	NH-A	brain
50	chr11:47606200-47612000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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