Variant report

Variant	rs11042541
Chromosome Location	chr11:9929477-9929478
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:9928185..9930607-chr11:9931281..9933826,2	MCF-7	breast:
2	chr11:9926975..9929844-chr11:10324322..10328573,4	MCF-7	breast:
3	chr11:9918384..9921801-chr11:9925480..9929741,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000148926	Chromatin interaction
ENSG00000254554	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10743120	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10770070	0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10770072	0.93[CHB][hapmap];0.93[JPT][hapmap]
rs10770073	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10840316	0.90[ASN][1000 genomes]
rs10840319	0.85[EUR][1000 genomes]
rs10840320	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840321	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10840322	0.92[AFR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11042527	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11042531	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11042532	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11042540	0.85[EUR][1000 genomes]
rs12360818	0.81[CHB][hapmap]
rs12362504	0.91[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12796169	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs4910073	0.96[ASN][1000 genomes]
rs4910074	0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4910076	0.92[CHB][hapmap]
rs55813311	0.87[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56138865	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs56165961	0.97[ASN][1000 genomes]
rs6483805	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6483809	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7105337	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7119074	0.85[EUR][1000 genomes]
rs7126063	0.93[CHB][hapmap]
rs7130681	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs7130923	1.00[CHB][hapmap]
rs71463738	0.93[ASN][1000 genomes]
rs7930281	0.93[CHB][hapmap];0.84[JPT][hapmap]
rs7931062	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7936793	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7949582	0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7950655	0.86[CHB][hapmap]
rs9300099	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9300100	0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs9332432	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9919605	0.93[CHB][hapmap];0.84[JPT][hapmap]

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	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	esv2762895	chr11:9849511-9954549	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv896988	chr11:9912052-10012511	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1041148	chr11:9927980-9954537	ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv976477	chr11:9929222-9945590	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9878800-9952200	Weak transcription	Aorta	Aorta
2	chr11:9882400-9929600	Weak transcription	Primary T cells from cord blood	blood
3	chr11:9894400-9978600	Weak transcription	Left Ventricle	heart
4	chr11:9904000-9937000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr11:9910000-9954600	Weak transcription	Pancreas	Pancrea
6	chr11:9915000-9937200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr11:9916600-9932600	Weak transcription	Fetal Intestine Small	intestine
8	chr11:9916800-9944400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr11:9916800-9944400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr11:9917000-9937200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr11:9917600-9933200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr11:9917600-9934200	Weak transcription	Skeletal Muscle Female	skeletal muscle
13	chr11:9917600-9951800	Weak transcription	Stomach Smooth Muscle	stomach
14	chr11:9917600-9952400	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr11:9917800-9933200	Weak transcription	Primary hematopoietic stem cells	blood
16	chr11:9917800-9952600	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr11:9920000-9933200	Weak transcription	Fetal Stomach	stomach
18	chr11:9921400-9934400	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr11:9923400-9943600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr11:9923400-9952200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr11:9924000-9944400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:9925200-9930000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr11:9925200-9944400	Weak transcription	Ovary	ovary
24	chr11:9925400-9929600	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr11:9925400-9951000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr11:9925400-9952200	Weak transcription	Lung	lung
27	chr11:9926200-9929600	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr11:9926200-9929600	Enhancers	Muscle Satellite Cultured Cells	--
29	chr11:9926200-9929600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr11:9926200-9929600	Enhancers	Osteobl	bone
31	chr11:9926400-9929600	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr11:9926400-9929600	Enhancers	HSMMtube	muscle
33	chr11:9926400-9929600	Enhancers	NH-A	brain
34	chr11:9926400-9929600	Enhancers	NHLF	lung
35	chr11:9926400-9929800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr11:9927000-9929600	Enhancers	HSMM	muscle
37	chr11:9927800-9929600	Enhancers	HUES48 Cell Line	embryonic stem cell
38	chr11:9927800-9929600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr11:9927800-9944400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr11:9928000-9929600	Enhancers	iPS-20b Cell Line	embryonic stem cell
41	chr11:9928000-9929600	Enhancers	Breast Myoepithelial Primary Cells	Breast
42	chr11:9928000-9944200	Weak transcription	Cortex derived primary cultured neurospheres	brain
43	chr11:9928000-9944400	Weak transcription	Brain Anterior Caudate	brain
44	chr11:9928200-9929800	Enhancers	NHDF-Ad	bronchial
45	chr11:9928400-9944200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
46	chr11:9928600-9929600	Flanking Active TSS	A549	lung
47	chr11:9928600-9938200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr11:9928600-9944200	Weak transcription	Adipose Nuclei	Adipose
49	chr11:9928800-9929800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr11:9928800-9931000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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