Variant report

Variant	rs17140396
Chromosome Location	chr3:120394521-120394522
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:120392100..120394815-chr3:120399111..120401774,2	MCF-7	breast:
2	chr3:120380414..120382961-chr3:120391984..120394900,2	MCF-7	breast:
3	chr3:120392048..120394831-chr3:120397080..120399083,3	K562	blood:

Variant related genes	Relation type
ENSG00000113924	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs17140364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17140367	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676817	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676818	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676819	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795573	0.86[AFR][1000 genomes]
rs61795577	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795582	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795590	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795596	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795597	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795599	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801736	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007557	chr3:119892894-120764353	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv536706	chr3:119892894-120764353	Flanking Bivalent TSS/Enh Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv1006428	chr3:120015620-120421982	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
4	esv3369381	chr3:120066425-120425510	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	esv3350409	chr3:120066445-120425480	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	esv3373301	chr3:120273762-120421260	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
7	nsv877377	chr3:120287683-120426750	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
8	esv3464294	chr3:120303062-120420810	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
9	esv3464295	chr3:120303062-120420810	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	diseases
10	nsv829699	chr3:120308332-120484695	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	19 gene(s)	inside rSNPs	diseases
11	nsv869548	chr3:120320731-121076337	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
12	nsv916869	chr3:120360281-120973169	Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
13	nsv877378	chr3:120381530-120606438	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120346400-120402200	Weak transcription	Gastric	stomach
2	chr3:120347400-120398000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr3:120370200-120396600	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:120378200-120396600	Weak transcription	Fetal Intestine Small	intestine
5	chr3:120381000-120396600	Weak transcription	Stomach Mucosa	stomach
6	chr3:120383400-120396800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr3:120385000-120396600	Weak transcription	Fetal Intestine Large	intestine
8	chr3:120387400-120395000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr3:120387600-120394600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:120389400-120396800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:120389600-120398600	Weak transcription	Pancreas	Pancrea
12	chr3:120389800-120396800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr3:120391400-120395200	Strong transcription	A549	lung
14	chr3:120391800-120400000	Weak transcription	Colonic Mucosa	Colon
15	chr3:120392200-120397000	Weak transcription	Brain Anterior Caudate	brain
16	chr3:120392400-120396600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:120392600-120396800	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:120393000-120396600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr3:120393000-120397000	Weak transcription	Brain Germinal Matrix	brain
20	chr3:120393000-120397200	Weak transcription	Fetal Brain Female	brain
21	chr3:120393200-120396600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:120393400-120397000	Weak transcription	Small Intestine	intestine
23	chr3:120393800-120395000	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr3:120393800-120396600	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr3:120393800-120397200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr3:120394200-120396800	Genic enhancers	Liver	Liver
27	chr3:120394200-120397000	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:120394400-120395800	Genic enhancers	HepG2	liver
29	chr3:120394400-120396600	Enhancers	iPS-18 Cell Line	embryonic stem cell

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