Variant report

Variant	rs11229868
Chromosome Location	chr11:58953775-58953776
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:58938579..58939084-chr11:58953392..58953945,2	MCF-7	breast:
2	chr11:58939464..58940365-chr11:58953507..58954250,4	MCF-7	breast:
3	chr11:58938470..58939572-chr11:58953440..58954576,4	K562	blood:
4	chr11:58938627..58939484-chr11:58953741..58954380,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110042	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1048696	1.00[CEU][hapmap];0.84[CHB][hapmap];0.93[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10501375	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10501376	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10896949	0.80[EUR][1000 genomes]
rs10896950	0.80[EUR][1000 genomes]
rs10896957	0.85[EUR][1000 genomes]
rs11229869	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229870	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11229872	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229873	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11229874	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229875	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11229882	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11229889	0.88[CEU][hapmap];0.88[MEX][hapmap];0.96[TSI][hapmap]
rs11229901	0.85[EUR][1000 genomes]
rs11229902	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11229903	1.00[CEU][hapmap];0.89[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs11229904	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12223401	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12284370	0.80[EUR][1000 genomes]
rs12575770	0.85[EUR][1000 genomes]
rs12576150	0.85[EUR][1000 genomes]
rs12576412	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs12576558	0.80[EUR][1000 genomes]
rs12576879	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12577252	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17153538	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1938595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35654554	0.85[EUR][1000 genomes]
rs3740946	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3781796	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59466005	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60265864	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61086875	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7104296	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7104437	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7926933	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7942203	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs869155	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1050013	chr11:58394598-59221090	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription 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	67 gene(s)	inside rSNPs	diseases
2	nsv948365	chr11:58515163-59156405	Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	esv2758272	chr11:58700092-59008673	Bivalent/Poised TSS Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	esv2759830	chr11:58700092-59008673	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
5	esv1821250	chr11:58925860-59059179	Enhancers Flanking Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11229868	WDR74	cis	parietal	SCAN
rs11229868	MPEG1	cis	lymphoblastoid	seeQTL
rs11229868	CCDC86	cis	parietal	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:58941600-58964000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr11:58943400-58954800	Weak transcription	Hela-S3	cervix
3	chr11:58943600-58975400	Weak transcription	NHEK	skin
4	chr11:58947600-58955000	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr11:58949400-58973400	Weak transcription	Right Ventricle	heart
6	chr11:58950000-58978400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr11:58950200-58958600	Weak transcription	Aorta	Aorta
8	chr11:58950400-58953800	Enhancers	Brain Hippocampus Middle	brain
9	chr11:58950400-58957400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:58950400-58972200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr11:58950800-58955800	Enhancers	Brain Cingulate Gyrus	brain
12	chr11:58950800-58957400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr11:58950800-58957800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr11:58951000-58955400	Enhancers	Brain Angular Gyrus	brain
15	chr11:58951000-58955800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr11:58951000-58956000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
17	chr11:58951000-58956200	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr11:58951000-58956600	Enhancers	Stomach Smooth Muscle	stomach
19	chr11:58951400-58954000	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr11:58951400-58954400	Enhancers	Brain Anterior Caudate	brain
21	chr11:58951400-58957200	Enhancers	Placenta	Placenta
22	chr11:58951600-58954800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr11:58951600-58954800	Enhancers	Colon Smooth Muscle	Colon
24	chr11:58951600-58957800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr11:58951800-58953800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr11:58951800-58953800	Weak transcription	Gastric	stomach
27	chr11:58951800-58955000	Enhancers	Sigmoid Colon	Sigmoid Colon
28	chr11:58951800-58955000	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr11:58951800-58955200	Enhancers	Placenta Amnion	Placenta Amnion
30	chr11:58951800-58955400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr11:58951800-58957200	Enhancers	Adipose Nuclei	Adipose
32	chr11:58952000-58954000	Weak transcription	Small Intestine	intestine
33	chr11:58952000-58954000	Weak transcription	NHLF	lung
34	chr11:58952000-58954800	Genic enhancers	Fetal Lung	lung
35	chr11:58952200-58953800	Enhancers	iPS-18 Cell Line	embryonic stem cell
36	chr11:58952200-58953800	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr11:58952200-58954400	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr11:58952200-58954800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr11:58952200-58954800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
40	chr11:58952200-58955600	Enhancers	Fetal Muscle Leg	muscle
41	chr11:58952400-58953800	Enhancers	Fetal Brain Male	brain
42	chr11:58952400-58953800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
43	chr11:58952400-58955000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr11:58952400-58960200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr11:58952600-58954000	Enhancers	Right Atrium	heart
46	chr11:58952600-58954200	Enhancers	Brain Germinal Matrix	brain
47	chr11:58952600-58955400	Weak transcription	Primary B cells from cord blood	blood
48	chr11:58952600-58957600	Enhancers	Lung	lung
49	chr11:58952800-58953800	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr11:58952800-58953800	Transcr. at gene 5' and 3'	Fetal Intestine Small	intestine

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