Variant report

Variant	rs11039112
Chromosome Location	chr11:47174296-47174297
allele	C/T
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	CTCF	chr11:47174260-47174410	AG04450	lung:	n/a	n/a
2	CTCF	chr11:47173779-47175556	SK-N-SH	brain:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47173836-47173844 chr11:47174821-47174837
3	RAD21	chr11:47174238-47175127	H1-hESC	embryonic stem cell:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
4	CTCF	chr11:47174015-47175271	A549	lung:	n/a	chr11:47174815-47174836 chr11:47174822-47174835 chr11:47174820-47174838 chr11:47174821-47174837
5	RAD21	chr11:47173739-47175488	SK-N-SH	brain:	n/a	chr11:47174818-47174837 chr11:47174697-47174709 chr11:47174822-47174836 chr11:47174824-47174833
6	POLR2A	chr11:47173928-47175390	HepG2	liver:	n/a	n/a
7	CEBPB	chr11:47174286-47174957	IMR90	lung:	n/a	n/a
8	CTCF	chr11:47174240-47174390	AG04449	skin:	n/a	n/a
9	POLR2A	chr11:47173818-47175361	Hela-S3	cervix:	n/a	n/a
10	SMC3	chr11:47174207-47175551	SK-N-SH	brain:	n/a	chr11:47174380-47174388 chr11:47174822-47174836 chr11:47174557-47174564

No.	Distal block	Cell Line	Cell type
1	chr11:46941180..46942052-chr11:47174287..47175251,5	K562	blood:
2	chr11:47173854..47175804-chr11:47178111..47180557,3	K562	blood:
3	chr11:46910320..46911827-chr11:47174259..47175968,19	MCF-7	breast:
4	chr11:46910929..46911796-chr11:47174261..47175544,7	MCF-7	breast:
5	chr11:46916008..46916655-chr11:47174120..47174871,2	K562	blood:
6	chr11:46939620..46940210-chr11:47174225..47174749,2	MCF-7	breast:
7	chr11:47162453..47166224-chr11:47170564..47174791,5	MCF-7	breast:

Variant related genes	Relation type
C11orf49	TF binding region
ENSG00000134569	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10466478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10501319	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap]
rs1055447	0.86[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs1060573	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10769225	0.82[CHB][hapmap]
rs10769226	0.83[CHB][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap]
rs10769227	0.83[CHB][hapmap]
rs10769230	0.83[ASN][1000 genomes]
rs10769233	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10769234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10769239	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838640	0.83[CHB][hapmap]
rs10838644	0.83[CHB][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap]
rs10838646	0.83[CHB][hapmap]
rs10838652	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs10838654	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10838658	0.82[CHB][hapmap]
rs10838659	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838660	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10838662	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.83[MEX][hapmap]
rs10838663	0.83[CHB][hapmap];0.80[CHD][hapmap]
rs10838664	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs11039074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039086	0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039097	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11039105	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039107	0.92[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11039119	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039124	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11039134	0.87[ASN][1000 genomes]
rs11600668	0.88[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11601798	0.85[CHB][hapmap]
rs12224096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12291341	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12417519	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs12574410	0.86[CHB][hapmap]
rs12796744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12807887	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1872896	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1965952	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1976142	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1976143	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2018527	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2029298	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2087215	0.83[CHB][hapmap];0.94[GIH][hapmap]
rs2279438	0.83[CHB][hapmap]
rs2279439	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs4237547	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4319472	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4394802	0.91[GIH][hapmap];0.82[MEX][hapmap]
rs4528282	0.82[CHB][hapmap]
rs4548577	0.83[CHB][hapmap]
rs4567413	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.83[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4579897	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4587689	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs4752815	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs4752816	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs4752951	0.82[CHB][hapmap]
rs4752952	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4752957	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4752962	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752963	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4752965	0.83[CHB][hapmap]
rs4752967	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4752969	0.83[CHB][hapmap];0.80[CHD][hapmap];0.94[GIH][hapmap];0.82[MEX][hapmap]
rs4752971	0.95[CEU][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57323109	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6485715	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs6485716	0.86[CHB][hapmap]
rs6485721	0.86[ASN][1000 genomes]
rs6485722	0.85[ASN][1000 genomes]
rs6485726	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs6485739	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7103581	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7108902	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7111270	0.83[CHB][hapmap]
rs7111764	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7112854	0.82[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7118546	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7119952	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7121418	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7124648	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7125807	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.86[ASN][1000 genomes]
rs7126005	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7128325	0.86[ASN][1000 genomes]
rs7128650	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs7130006	0.83[CHB][hapmap];0.86[GIH][hapmap]
rs7130947	0.83[CHB][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap]
rs747650	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7479189	1.00[CEU][hapmap];0.92[YRI][hapmap];0.89[ASN][1000 genomes]
rs7931260	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap]
rs7935346	0.91[GIH][hapmap]
rs7937101	0.95[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.84[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7937410	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7937950	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7940240	0.83[CHB][hapmap];0.88[GIH][hapmap]
rs7942473	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7945315	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7946709	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7947878	0.82[ASN][1000 genomes]
rs7950753	0.83[CHB][hapmap];0.91[GIH][hapmap]
rs923324	0.82[CHB][hapmap]
rs9633886	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11039112	C11orf49	cis	parietal	SCAN
rs11039112	F2	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:47143600-47175200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr11:47145200-47174800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr11:47153000-47174400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:47153400-47174800	Weak transcription	Primary hematopoietic stem cells	blood
5	chr11:47155600-47174400	Weak transcription	Fetal Brain Male	brain
6	chr11:47158000-47174800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr11:47158800-47175000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr11:47160000-47176400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr11:47161600-47174400	Weak transcription	Spleen	Spleen
10	chr11:47161600-47174600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr11:47161600-47176000	Weak transcription	Dnd41	blood
12	chr11:47164200-47175000	Weak transcription	HUVEC	blood vessel
13	chr11:47164400-47174400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
14	chr11:47165000-47184800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:47165000-47185000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr11:47165200-47185600	Weak transcription	Aorta	Aorta
17	chr11:47165400-47177600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr11:47165400-47188600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr11:47165600-47177600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr11:47165600-47177800	Weak transcription	NHEK	skin
21	chr11:47168600-47177800	Weak transcription	A549	lung
22	chr11:47169200-47176000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:47170000-47174400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
24	chr11:47170800-47174400	Weak transcription	Colonic Mucosa	Colon
25	chr11:47170800-47174400	Weak transcription	HepG2	liver
26	chr11:47170800-47176800	Weak transcription	Lung	lung
27	chr11:47171000-47174600	Weak transcription	Stomach Mucosa	stomach
28	chr11:47171000-47175200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr11:47171000-47177200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr11:47171000-47177600	Weak transcription	Esophagus	oesophagus
31	chr11:47171000-47183400	Weak transcription	Gastric	stomach
32	chr11:47171200-47174400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:47171200-47174400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr11:47171200-47174400	Weak transcription	Left Ventricle	heart
35	chr11:47171200-47176000	Weak transcription	Fetal Brain Female	brain
36	chr11:47171200-47177600	Weak transcription	Ovary	ovary
37	chr11:47171400-47174400	Weak transcription	Brain Angular Gyrus	brain
38	chr11:47171400-47174400	Weak transcription	Right Ventricle	heart
39	chr11:47171400-47174400	Weak transcription	Small Intestine	intestine
40	chr11:47171400-47174400	Weak transcription	HSMM	muscle
41	chr11:47171400-47174800	Weak transcription	Fetal Heart	heart
42	chr11:47171400-47174800	Weak transcription	Hela-S3	cervix
43	chr11:47171400-47186000	Weak transcription	Rectal Smooth Muscle	rectum
44	chr11:47171600-47174400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr11:47171600-47174400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr11:47171600-47174400	Weak transcription	Duodenum Smooth Muscle	Duodenum
47	chr11:47171600-47186400	Weak transcription	Psoas Muscle	Psoas
48	chr11:47171800-47174400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr11:47171800-47174400	Weak transcription	Brain Germinal Matrix	brain
50	chr11:47171800-47174400	Weak transcription	Colon Smooth Muscle	Colon

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