Variant report

Variant	rs2773344
Chromosome Location	chr9:100359073-100359074
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:100210584..100212348-chr9:100357431..100359264,2	MCF-7	breast:
2	chr9:100358063..100359850-chr9:100366510..100368844,2	MCF-7	breast:
3	chr9:100357473..100360015-chr9:100394400..100396329,2	K562	blood:
4	chr9:100248103..100250709-chr9:100357540..100361219,3	MCF-7	breast:
5	chr9:100357134..100359474-chr9:100365218..100367036,2	K562	blood:

Variant related genes	Relation type
ENSG00000136937	Chromatin interaction
ENSG00000136925	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10123528	1.00[JPT][hapmap]
rs16922598	1.00[JPT][hapmap]
rs1962592	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2149984	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245694	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2254733	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773343	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773349	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2773358	0.99[EUR][1000 genomes]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805778	1.00[JPT][hapmap]
rs2805783	0.85[CEU][hapmap];0.81[EUR][1000 genomes]
rs2805785	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2805786	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805787	0.93[EUR][1000 genomes]
rs2805788	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805792	0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805793	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805802	0.82[EUR][1000 genomes]
rs2805831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2805834	0.88[AMR][1000 genomes]
rs2805835	1.00[JPT][hapmap]
rs2808669	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2808676	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2808682	1.00[JPT][hapmap]
rs7863516	0.88[ASN][1000 genomes]
rs932916	0.89[EUR][1000 genomes];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	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100333600-100361800	Weak transcription	Gastric	stomach
2	chr9:100336200-100360000	Weak transcription	Brain Substantia Nigra	brain
3	chr9:100338400-100361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr9:100338600-100360800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr9:100346200-100360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr9:100350400-100361800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr9:100350600-100360800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr9:100351200-100361800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr9:100353000-100362800	Weak transcription	Esophagus	oesophagus
11	chr9:100353200-100362200	Enhancers	Fetal Brain Male	brain
12	chr9:100353200-100363200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr9:100353400-100359200	Strong transcription	K562	blood
14	chr9:100354000-100360800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr9:100354000-100360800	Weak transcription	Lung	lung
16	chr9:100354200-100360600	Weak transcription	GM12878-XiMat	blood
17	chr9:100354800-100363000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr9:100355000-100360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr9:100355000-100360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr9:100355000-100360800	Enhancers	Skeletal Muscle Male	skeletal muscle
21	chr9:100355400-100360800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr9:100355600-100359200	Weak transcription	Brain Germinal Matrix	brain
23	chr9:100356600-100361400	Enhancers	Brain Hippocampus Middle	brain
24	chr9:100356800-100362400	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:100357000-100359400	Weak transcription	Adipose Nuclei	Adipose
26	chr9:100357000-100360200	Weak transcription	Right Ventricle	heart
27	chr9:100357000-100362800	Weak transcription	HSMM	muscle
28	chr9:100357200-100360800	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr9:100357200-100360800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr9:100357200-100363000	Weak transcription	Pancreas	Pancrea
31	chr9:100357200-100363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr9:100357400-100359400	Weak transcription	Fetal Stomach	stomach
33	chr9:100357400-100360600	Weak transcription	Fetal Muscle Leg	muscle
34	chr9:100357400-100360800	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr9:100357400-100360800	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr9:100357400-100363000	Weak transcription	HSMMtube	muscle
37	chr9:100357800-100360800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr9:100358400-100359200	Genic enhancers	Ovary	ovary
39	chr9:100358400-100359200	Enhancers	Psoas Muscle	Psoas
40	chr9:100358400-100359400	Enhancers	Brain Angular Gyrus	brain
41	chr9:100358400-100359400	Enhancers	Left Ventricle	heart
42	chr9:100358400-100362000	Enhancers	Right Atrium	heart
43	chr9:100358600-100359400	Genic enhancers	Fetal Heart	heart
44	chr9:100358600-100359600	Enhancers	Colon Smooth Muscle	Colon
45	chr9:100358600-100360000	Weak transcription	Fetal Muscle Trunk	muscle
46	chr9:100358600-100360800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr9:100358600-100360800	Enhancers	Brain Anterior Caudate	brain
48	chr9:100358600-100361000	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr9:100358600-100361400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
50	chr9:100358600-100361600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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