Variant report

Variant	rs2780960
Chromosome Location	chr9:103337550-103337551
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:103334520..103337877-chr9:103341239..103344703,3	MCF-7	breast:
2	chr9:103324824..103326830-chr9:103336259..103338529,2	MCF-7	breast:
3	chr9:103114539..103116282-chr9:103335950..103338864,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200966	Chromatin interaction
ENSG00000136891	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12002878	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12005789	0.89[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1226587	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]
rs1226589	0.84[AMR][1000 genomes]
rs1226590	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]
rs1226591	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]
rs1226592	0.82[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1226593	0.80[AMR][1000 genomes]
rs1236813	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1628249	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17742370	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2151597	0.82[CEU][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2184201	0.82[AMR][1000 genomes]
rs2483624	0.81[AMR][1000 genomes]
rs2780954	1.00[ASN][1000 genomes]
rs2780955	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2780956	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800280	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800281	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800282	0.84[AMR][1000 genomes]
rs2800283	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2800284	0.82[AMR][1000 genomes]
rs2800285	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2800289	1.00[ASN][1000 genomes]
rs2800290	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57290629	0.95[ASN][1000 genomes]
rs60422299	0.95[ASN][1000 genomes]
rs951868	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv893623	chr9:102648036-103405197	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS 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 target site	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:103261600-103340200	Weak transcription	Left Ventricle	heart
2	chr9:103273600-103337600	Weak transcription	NHDF-Ad	bronchial
3	chr9:103307400-103341800	Strong transcription	HUES48 Cell Line	embryonic stem cell
4	chr9:103307400-103347800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr9:103308000-103340200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:103308600-103345400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr9:103311800-103342400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr9:103313200-103340800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr9:103318400-103342400	Weak transcription	Brain Anterior Caudate	brain
10	chr9:103318600-103344000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr9:103322400-103340400	Weak transcription	Brain Substantia Nigra	brain
12	chr9:103322600-103341800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
13	chr9:103323000-103340200	Weak transcription	Brain Hippocampus Middle	brain
14	chr9:103323400-103342000	Weak transcription	Brain Angular Gyrus	brain
15	chr9:103323800-103340600	Weak transcription	Brain Inferior Temporal Lobe	brain
16	chr9:103324000-103340200	Weak transcription	Cortex derived primary cultured neurospheres	brain
17	chr9:103324800-103345400	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:103325600-103337600	Weak transcription	NHLF	lung
19	chr9:103326400-103337800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:103327800-103349400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr9:103329600-103360800	Weak transcription	Aorta	Aorta
22	chr9:103329800-103351800	Weak transcription	Ovary	ovary
23	chr9:103330000-103357800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr9:103330400-103345400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr9:103330400-103351600	Weak transcription	Fetal Stomach	stomach
26	chr9:103330800-103349400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr9:103331600-103360200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr9:103332400-103351600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr9:103332400-103357600	Weak transcription	Fetal Lung	lung
30	chr9:103333600-103360800	Weak transcription	Fetal Brain Male	brain
31	chr9:103334200-103337600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr9:103334200-103338200	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr9:103334200-103341200	Strong transcription	HUES6 Cell Line	embryonic stem cell
34	chr9:103334200-103351000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr9:103334600-103350600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr9:103334800-103350200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:103335000-103338600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr9:103335000-103351000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr9:103335400-103341400	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr9:103335600-103341200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr9:103336000-103339000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr9:103336200-103338000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr9:103336400-103340200	Enhancers	HSMM	muscle
44	chr9:103336600-103337600	Enhancers	Muscle Satellite Cultured Cells	--
45	chr9:103336600-103337600	Weak transcription	NHEK	skin
46	chr9:103336600-103337800	Weak transcription	HMEC	breast
47	chr9:103336600-103338400	Strong transcription	Fetal Brain Female	brain
48	chr9:103336800-103338000	Enhancers	HSMMtube	muscle
49	chr9:103336800-103338600	Enhancers	Fetal Muscle Leg	muscle
50	chr9:103336800-103347800	Weak transcription	Brain Germinal Matrix	brain

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