Variant report

Variant	rs580501
Chromosome Location	chr9:14117221-14117222
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	chr9:14117034..14118965-chr9:14313015..14315569,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000147862	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10756530	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810093	0.95[CEU][hapmap];0.82[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10810095	0.81[EUR][1000 genomes]
rs35870361	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs497789	0.81[CEU][hapmap];0.87[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs508940	0.86[CEU][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs510777	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs516075	0.83[CHB][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs516090	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs574460	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs580845	0.87[CHB][hapmap]
rs7019649	0.95[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7034211	0.90[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7862890	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1033764	chr9:13764918-14226168	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription 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 target site	8 gene(s)	inside rSNPs	diseases
2	nsv892593	chr9:13948798-14233159	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh 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	nsv1023303	chr9:14025605-14286269	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	nsv540069	chr9:14025605-14286269	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv1029491	chr9:14033607-14942373	Enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv429998	chr9:14043516-14214688	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:14096800-14120000	Weak transcription	Brain Substantia Nigra	brain
2	chr9:14097400-14135400	Weak transcription	HSMMtube	muscle
3	chr9:14101800-14128200	Weak transcription	Esophagus	oesophagus
4	chr9:14103200-14122800	Weak transcription	Brain Anterior Caudate	brain
5	chr9:14103400-14128400	Weak transcription	Brain Angular Gyrus	brain
6	chr9:14103600-14119800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr9:14104800-14118600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr9:14107000-14126400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:14108000-14127400	Weak transcription	Stomach Mucosa	stomach
10	chr9:14108400-14118200	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr9:14108400-14119800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
12	chr9:14108400-14120000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr9:14108400-14121000	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr9:14108600-14118600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr9:14108800-14143800	Weak transcription	Fetal Intestine Small	intestine
16	chr9:14109000-14120800	Strong transcription	Liver	Liver
17	chr9:14109600-14120200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr9:14110000-14128400	Weak transcription	Fetal Kidney	kidney
19	chr9:14110200-14127200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr9:14111000-14118400	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:14111200-14121600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr9:14111400-14124200	Weak transcription	Spleen	Spleen
23	chr9:14111600-14118000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr9:14111800-14117600	Strong transcription	Brain Germinal Matrix	brain
25	chr9:14112000-14118400	Strong transcription	HSMM	muscle
26	chr9:14112000-14121200	Strong transcription	Adipose Nuclei	Adipose
27	chr9:14112200-14118400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr9:14112200-14119400	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr9:14112200-14120200	Strong transcription	HUVEC	blood vessel
30	chr9:14112400-14117400	Strong transcription	Duodenum Smooth Muscle	Duodenum
31	chr9:14112400-14118400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr9:14112400-14119400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr9:14112400-14119400	Weak transcription	Fetal Intestine Large	intestine
34	chr9:14112400-14119600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr9:14112600-14121400	Strong transcription	Fetal Muscle Leg	muscle
36	chr9:14112800-14120600	Strong transcription	Duodenum Mucosa	Duodenum
37	chr9:14114000-14120200	Strong transcription	Fetal Lung	lung
38	chr9:14114400-14118800	Strong transcription	HMEC	breast
39	chr9:14114400-14125200	Weak transcription	Colonic Mucosa	Colon
40	chr9:14115000-14120600	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr9:14115400-14117800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr9:14115400-14127000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr9:14115600-14117800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr9:14115600-14120800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr9:14115800-14118400	Strong transcription	Colon Smooth Muscle	Colon
46	chr9:14116000-14118000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr9:14116200-14127000	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr9:14116400-14117800	Weak transcription	Placenta	Placenta
49	chr9:14116400-14117800	Weak transcription	A549	lung
50	chr9:14116400-14119800	Weak transcription	Fetal Brain Male	brain

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