Variant report

Variant	rs17023420
Chromosome Location	chr2:98486816-98486817
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98485446..98487347-chr2:98611436..98613379,2	MCF-7	breast:
2	chr2:98481137..98483396-chr2:98485163..98486842,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1026015	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1446326	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022373	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022581	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17022797	1.00[EUR][1000 genomes]
rs17022803	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17025147	0.85[EUR][1000 genomes]
rs17025319	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs2309314	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61729688	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704792	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6737466	1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs6748814	1.00[EUR][1000 genomes]
rs72942819	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98447800-98502800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr2:98478600-98502200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr2:98478600-98502800	Weak transcription	Colonic Mucosa	Colon
4	chr2:98478600-98502800	Weak transcription	Pancreas	Pancrea
5	chr2:98478800-98489800	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:98483800-98487600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:98484000-98487200	Enhancers	Left Ventricle	heart
8	chr2:98484000-98487800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr2:98484000-98489200	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr2:98484600-98487200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
11	chr2:98484800-98487200	Enhancers	HUES64 Cell Line	embryonic stem cell
12	chr2:98485000-98487200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:98485000-98487200	Enhancers	Fetal Muscle Leg	muscle
14	chr2:98485000-98487400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr2:98485000-98487400	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr2:98485000-98487400	Enhancers	Right Atrium	heart
17	chr2:98485000-98487600	Enhancers	Duodenum Mucosa	Duodenum
18	chr2:98485000-98487800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:98485000-98487800	Enhancers	Fetal Heart	heart
20	chr2:98485000-98487800	Enhancers	Fetal Thymus	thymus
21	chr2:98485000-98487800	Enhancers	Monocytes-CD14+_RO01746	blood
22	chr2:98485000-98488200	Enhancers	Primary monocytes fromperipheralblood	blood
23	chr2:98485000-98488200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr2:98485000-98488400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:98485000-98488400	Enhancers	Stomach Mucosa	stomach
26	chr2:98485200-98487000	Enhancers	ES-I3 Cell Line	embryonic stem cell
27	chr2:98485200-98487200	Enhancers	Right Ventricle	heart
28	chr2:98485200-98487400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:98485200-98487400	Enhancers	Spleen	Spleen
30	chr2:98485200-98487600	Enhancers	Brain Hippocampus Middle	brain
31	chr2:98485200-98487800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr2:98485200-98487800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
33	chr2:98485200-98488000	Enhancers	HepG2	liver
34	chr2:98485200-98488200	Enhancers	Thymus	Thymus
35	chr2:98485200-98488400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:98485400-98487200	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr2:98485400-98487200	Flanking Active TSS	NH-A	brain
38	chr2:98485400-98487400	Enhancers	Cortex derived primary cultured neurospheres	brain
39	chr2:98485400-98488000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr2:98485600-98487000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:98485600-98487000	Flanking Active TSS	HMEC	breast
42	chr2:98485600-98487200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr2:98485600-98487200	Enhancers	Fetal Intestine Small	intestine
44	chr2:98485600-98487600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr2:98485600-98488000	Enhancers	Brain Angular Gyrus	brain
46	chr2:98485600-98488400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr2:98485600-98488400	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr2:98485600-98488600	Enhancers	Duodenum Smooth Muscle	Duodenum
49	chr2:98485600-98488600	Enhancers	Placenta	Placenta
50	chr2:98485800-98487200	Enhancers	Aorta	Aorta

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