Variant report

Variant	rs17240621
Chromosome Location	chr3:120407583-120407584
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:120406419..120409773-chr3:120409851..120413198,4	MCF-7	breast:
2	chr3:120402292..120405361-chr3:120406380..120408889,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs16831690	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs378561	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs424413	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4676823	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4676824	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs537922	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61795615	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61796373	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs61796376	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs624496	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6785511	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6801062	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7430753	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7612975	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs836215	0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs883537	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9850589	1.00[EUR][1000 genomes];1.00[ASN][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:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:120397600-120421600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr3:120397800-120410600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr3:120397800-120410600	Weak transcription	Brain Angular Gyrus	brain
4	chr3:120397800-120412200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr3:120397800-120415800	Weak transcription	Ovary	ovary
6	chr3:120397800-120420600	Weak transcription	Primary B cells from cord blood	blood
7	chr3:120397800-120421800	Weak transcription	Aorta	Aorta
8	chr3:120397800-120424800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:120398200-120408000	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr3:120398200-120408200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr3:120398200-120408200	Weak transcription	Skeletal Muscle Female	skeletal muscle
12	chr3:120398200-120410400	Weak transcription	Brain Substantia Nigra	brain
13	chr3:120398200-120412200	Weak transcription	Brain Hippocampus Middle	brain
14	chr3:120398200-120412200	Weak transcription	HMEC	breast
15	chr3:120398200-120415200	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr3:120398200-120423200	Weak transcription	Psoas Muscle	Psoas
17	chr3:120398200-120427000	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:120398200-120427800	Weak transcription	Placenta	Placenta
19	chr3:120398200-120430200	Weak transcription	NHEK	skin
20	chr3:120398200-120438000	Weak transcription	Skeletal Muscle Male	skeletal muscle
21	chr3:120398400-120412200	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr3:120398400-120412400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr3:120398600-120411800	Weak transcription	HUVEC	blood vessel
24	chr3:120398800-120442200	Weak transcription	Fetal Muscle Leg	muscle
25	chr3:120400000-120410600	Weak transcription	Hela-S3	cervix
26	chr3:120400000-120412200	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr3:120400200-120421600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr3:120400400-120407800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr3:120400800-120407800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:120401000-120424800	Weak transcription	Rectal Smooth Muscle	rectum
31	chr3:120401200-120411200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:120401600-120407600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:120402000-120408000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr3:120402200-120408200	Weak transcription	Duodenum Mucosa	Duodenum
35	chr3:120402200-120411800	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:120402200-120412200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr3:120402400-120407600	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr3:120402400-120407800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr3:120402400-120423600	Weak transcription	Lung	lung
40	chr3:120402600-120408000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr3:120402600-120410400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr3:120402600-120420800	Weak transcription	Primary hematopoietic stem cells	blood
43	chr3:120402800-120408200	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:120402800-120412200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
45	chr3:120402800-120421800	Weak transcription	Fetal Kidney	kidney
46	chr3:120402800-120456600	Weak transcription	Sigmoid Colon	Sigmoid Colon
47	chr3:120403200-120408000	Weak transcription	HepG2	liver
48	chr3:120403200-120408400	Weak transcription	Liver	Liver
49	chr3:120403200-120412000	Weak transcription	Fetal Intestine Small	intestine
50	chr3:120403600-120423800	Weak transcription	Spleen	Spleen

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