Variant report

Variant	rs11539461
Chromosome Location	chr14:77935659-77935660
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:77922040..77925665-chr14:77935403..77938131,3	MCF-7	breast:
2	chr14:77923271..77925943-chr14:77932177..77936062,3	K562	blood:
3	chr14:77934304..77936307-chr14:78175272..78177718,2	K562	blood:
4	chr14:77921860..77928400-chr14:77931824..77937732,8	MCF-7	breast:
5	chr14:77934807..77937271-chr14:78175752..78177718,2	K562	blood:
6	chr14:77935395..77937694-chr14:77986680..77989450,2	K562	blood:

Variant related genes	Relation type
ENSG00000151445	Chromatin interaction
ENSG00000100591	Chromatin interaction
ENSG00000119705	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10149037	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11159261	1.00[JPT][hapmap]
rs11624314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11844300	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12432582	0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12433521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12434419	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12435136	1.00[JPT][hapmap]
rs12435676	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12897689	1.00[ASN][1000 genomes]
rs13379432	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17751406	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17751412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824034	1.00[JPT][hapmap]
rs17824214	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17824322	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2063997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs28583775	0.86[ASN][1000 genomes]
rs34180883	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3742737	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3783985	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4899652	1.00[JPT][hapmap]
rs4903578	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4903579	1.00[JPT][hapmap]
rs4903580	1.00[JPT][hapmap]
rs4903581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6574374	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7149534	1.00[ASN][1000 genomes]
rs7155063	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7156032	1.00[CHB][hapmap]
rs7156671	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8007503	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs8010520	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs8017215	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8018509	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9323643	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]

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	nsv1041985	chr14:77877421-77936969	Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11539461	ENSG00000100591	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:77925600-77936600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:77925800-77936400	Strong transcription	Fetal Muscle Trunk	muscle
3	chr14:77926000-77936200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr14:77926000-77936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr14:77926000-77936400	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr14:77926000-77936800	Strong transcription	H9 Cell Line	embryonic stem cell
7	chr14:77926000-77936800	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr14:77926000-77939000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr14:77926200-77935800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr14:77926200-77936000	Strong transcription	HUES64 Cell Line	embryonic stem cell
11	chr14:77926200-77936000	Strong transcription	NHDF-Ad	bronchial
12	chr14:77926200-77936200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:77926200-77936200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr14:77926200-77936200	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr14:77926200-77936200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr14:77926200-77936200	Strong transcription	Fetal Intestine Large	intestine
17	chr14:77926200-77936200	Strong transcription	Placenta	Placenta
18	chr14:77926200-77936200	Strong transcription	Fetal Thymus	thymus
19	chr14:77926200-77936200	Strong transcription	Lung	lung
20	chr14:77926200-77936200	Strong transcription	Monocytes-CD14+_RO01746	blood
21	chr14:77926200-77936400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr14:77926200-77936400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr14:77926200-77936400	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr14:77926200-77936400	Strong transcription	Skeletal Muscle Male	skeletal muscle
25	chr14:77926200-77936600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
26	chr14:77926200-77936800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr14:77926200-77936800	Strong transcription	Muscle Satellite Cultured Cells	--
28	chr14:77926200-77937000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr14:77926200-77937000	Strong transcription	Fetal Stomach	stomach
30	chr14:77926200-77937000	Strong transcription	Ovary	ovary
31	chr14:77926400-77935800	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
32	chr14:77926400-77935800	Strong transcription	Fetal Intestine Small	intestine
33	chr14:77926400-77936000	Strong transcription	Cortex derived primary cultured neurospheres	brain
34	chr14:77926400-77936000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr14:77926400-77936000	Strong transcription	HSMMtube	muscle
36	chr14:77926400-77936200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr14:77926400-77936200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr14:77926400-77936200	Strong transcription	Duodenum Mucosa	Duodenum
39	chr14:77926400-77936200	Strong transcription	Fetal Kidney	kidney
40	chr14:77926400-77936200	Strong transcription	Osteobl	bone
41	chr14:77926400-77936400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:77926400-77936400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr14:77926400-77936400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr14:77926400-77936400	Strong transcription	Adipose Nuclei	Adipose
45	chr14:77926400-77936400	Strong transcription	Fetal Brain Female	brain
46	chr14:77926400-77936400	Strong transcription	Sigmoid Colon	Sigmoid Colon
47	chr14:77926400-77936600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr14:77926400-77936600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr14:77926400-77936600	Strong transcription	Brain Hippocampus Middle	brain
50	chr14:77926400-77936800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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