Variant report

Variant	rs2772376
Chromosome Location	chr6:33416111-33416112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:33392146..33394863-chr6:33415963..33418099,3	MCF-7	breast:
2	chr6:33407430..33409237-chr6:33415034..33417664,3	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11757273	0.82[ASN][1000 genomes]
rs1613451	0.82[ASN][1000 genomes]
rs1755045	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1755046	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1755047	0.82[ASN][1000 genomes]
rs1755048	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1755049	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2076775	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs211456	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247385	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2274730	0.81[ASN][1000 genomes]
rs2480487	0.80[ASN][1000 genomes]
rs2747477	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs2747479	0.90[ASN][1000 genomes]
rs2772373	0.83[ASN][1000 genomes]
rs2772375	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2772387	0.80[ASN][1000 genomes]
rs2772389	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2772390	0.80[ASN][1000 genomes]
rs2772391	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2772392	0.81[ASN][1000 genomes]
rs3130025	0.80[ASN][1000 genomes]
rs411136	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs453590	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs461964	0.81[ASN][1000 genomes]
rs465223	0.81[ASN][1000 genomes]
rs465506	0.81[ASN][1000 genomes]
rs4711325	0.95[ASN][1000 genomes]
rs4713625	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66840884	0.81[ASN][1000 genomes]
rs7382303	0.81[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs9357159	0.81[ASN][1000 genomes]
rs9366822	0.80[ASN][1000 genomes]
rs9380355	0.81[ASN][1000 genomes]
rs9461856	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830637	chr6:33329365-33510704	Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv602832	chr6:33382241-33520221	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
3	nsv437503	chr6:33408542-33421577	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2772376	TAF11	cis	cerebellum	SCAN
rs2772376	SPDEF	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33399400-33421200	Weak transcription	HMEC	breast
2	chr6:33399400-33421600	Weak transcription	Stomach Mucosa	stomach
3	chr6:33399600-33421400	Weak transcription	HUVEC	blood vessel
4	chr6:33399800-33421400	Weak transcription	A549	lung
5	chr6:33400000-33418000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr6:33400000-33420600	Strong transcription	Brain Germinal Matrix	brain
7	chr6:33401200-33420800	Strong transcription	Fetal Brain Female	brain
8	chr6:33401400-33417600	Strong transcription	Primary T cells fromperipheralblood	blood
9	chr6:33401400-33418800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
10	chr6:33401400-33421400	Weak transcription	Right Atrium	heart
11	chr6:33401600-33416600	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr6:33402000-33417600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr6:33402000-33418000	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr6:33402000-33418000	Strong transcription	NHLF	lung
15	chr6:33402000-33418200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:33402000-33420600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr6:33402200-33417400	Strong transcription	Primary T helper cells fromperipheralblood	blood
18	chr6:33402200-33417400	Strong transcription	Thymus	Thymus
19	chr6:33402200-33418200	Strong transcription	Fetal Muscle Leg	muscle
20	chr6:33402200-33418600	Strong transcription	Dnd41	blood
21	chr6:33402200-33420000	Strong transcription	Fetal Thymus	thymus
22	chr6:33402200-33420800	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr6:33402400-33420800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr6:33402600-33417600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr6:33402600-33420000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:33402600-33420400	Strong transcription	Fetal Stomach	stomach
27	chr6:33402600-33421400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr6:33402800-33417200	Strong transcription	Fetal Intestine Small	intestine
29	chr6:33402800-33417400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr6:33402800-33417600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr6:33402800-33417600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr6:33402800-33417600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr6:33402800-33417800	Strong transcription	Primary T cells from cord blood	blood
34	chr6:33402800-33417800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr6:33402800-33418400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
36	chr6:33402800-33418600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr6:33402800-33418600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
38	chr6:33402800-33419000	Strong transcription	HUES48 Cell Line	embryonic stem cell
39	chr6:33402800-33420000	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr6:33402800-33420000	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr6:33402800-33420000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
42	chr6:33402800-33420200	Strong transcription	H1 Cell Line	embryonic stem cell
43	chr6:33402800-33420200	Strong transcription	Fetal Muscle Trunk	muscle
44	chr6:33403000-33418000	Strong transcription	Fetal Intestine Large	intestine
45	chr6:33403000-33418000	Strong transcription	Ovary	ovary
46	chr6:33403000-33418200	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr6:33403000-33420600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr6:33403200-33417200	Strong transcription	Placenta Amnion	Placenta Amnion
49	chr6:33403200-33418000	Strong transcription	Stomach Smooth Muscle	stomach
50	chr6:33403200-33420200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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