Variant report

Variant	rs61138004
Chromosome Location	chr3:20145855-20145856
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:20105530..20108149-chr3:20143893..20147714,3	MCF-7	breast:
2	chr3:20144778..20146752-chr3:20150014..20154937,5	K562	blood:
3	chr3:20080711..20083286-chr3:20145252..20149084,3	MCF-7	breast:
4	chr3:19987372..19989134-chr3:20145217..20148205,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144566	Chromatin interaction
ENSG00000114166	Chromatin interaction
ENSG00000163576	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs10084714	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061636	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124376	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11712709	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11715447	0.88[AFR][1000 genomes]
rs12488369	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488589	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490215	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17006610	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17006623	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797343	1.00[ASN][1000 genomes]
rs28716666	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34159701	1.00[ASN][1000 genomes]
rs3828352	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41285057	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417886	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56042248	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56117426	0.83[EUR][1000 genomes]
rs61457790	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs62241674	1.00[ASN][1000 genomes]
rs62241698	1.00[ASN][1000 genomes]
rs62243080	0.83[EUR][1000 genomes]
rs62243081	0.82[EUR][1000 genomes]
rs62243098	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs62243100	0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs62243131	0.98[EUR][1000 genomes]
rs6550307	0.83[EUR][1000 genomes]
rs6550339	0.80[EUR][1000 genomes]
rs67660889	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67713322	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771367	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771941	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774367	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791385	0.96[EUR][1000 genomes]
rs6793985	0.97[EUR][1000 genomes]
rs6807771	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618597	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7639282	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9819628	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819739	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828701	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836418	0.83[EUR][1000 genomes]
rs9852109	1.00[ASN][1000 genomes]
rs9855900	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857135	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1833006	chr3:19562271-20389045	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS 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	30 gene(s)	inside rSNPs	diseases
2	nsv1010613	chr3:19942032-20461486	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers 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 miRNA target site	28 gene(s)	inside rSNPs	diseases
3	esv1826030	chr3:19972766-20170581	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	esv1826830	chr3:19982972-20632072	Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	esv1829542	chr3:20009231-20384627	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
6	nsv834627	chr3:20068115-20227975	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
7	nsv433359	chr3:20090908-20587572	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv470450	chr3:20096735-20389045	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1001006	chr3:20110743-20752628	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv536512	chr3:20110743-20752628	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
11	esv1829018	chr3:20116077-20596244	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
12	esv1827700	chr3:20119716-20489086	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
13	esv1830036	chr3:20121828-20278275	Active TSS Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS 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 miRNA target site	15 gene(s)	inside rSNPs	diseases
14	esv1830599	chr3:20121828-20375643	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
15	nsv3719	chr3:20133243-20150202	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
16	esv1828816	chr3:20136508-20389045	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20123000-20153000	Weak transcription	Fetal Muscle Trunk	muscle
3	chr3:20123200-20153200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr3:20131800-20153000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr3:20132800-20152400	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr3:20137000-20150000	Weak transcription	K562	blood
9	chr3:20137400-20156600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr3:20137600-20153000	Weak transcription	Spleen	Spleen
11	chr3:20137800-20150200	Weak transcription	Lung	lung
12	chr3:20137800-20150200	Weak transcription	Right Ventricle	heart
13	chr3:20137800-20153000	Weak transcription	Esophagus	oesophagus
14	chr3:20137800-20153000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:20137800-20153200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr3:20138000-20150400	Weak transcription	Fetal Intestine Large	intestine
17	chr3:20138000-20152800	Weak transcription	Duodenum Mucosa	Duodenum
18	chr3:20138000-20153000	Weak transcription	Aorta	Aorta
19	chr3:20138000-20153000	Weak transcription	Fetal Muscle Leg	muscle
20	chr3:20138800-20148000	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr3:20138800-20152600	Weak transcription	Colon Smooth Muscle	Colon
22	chr3:20138800-20156400	Weak transcription	Rectal Smooth Muscle	rectum
23	chr3:20139000-20152800	Weak transcription	Liver	Liver
24	chr3:20139000-20152800	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr3:20139000-20164000	Weak transcription	Small Intestine	intestine
26	chr3:20139800-20147400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:20139800-20161000	Weak transcription	Fetal Intestine Small	intestine
28	chr3:20140600-20148600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
29	chr3:20141000-20150200	Weak transcription	Fetal Stomach	stomach
30	chr3:20141000-20153200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr3:20141200-20150200	Weak transcription	Pancreas	Pancrea
32	chr3:20141200-20153000	Weak transcription	Fetal Lung	lung
33	chr3:20141200-20167400	Weak transcription	HSMMtube	muscle
34	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr3:20141800-20153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr3:20141800-20153000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:20142200-20152600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
39	chr3:20143200-20148200	Enhancers	Primary T helper cells PMA-I stimulated	--
40	chr3:20143200-20150800	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr3:20143200-20152800	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr3:20143200-20152800	Weak transcription	Left Ventricle	heart
43	chr3:20143200-20153000	Weak transcription	Adipose Nuclei	Adipose
44	chr3:20143200-20153000	Weak transcription	Ovary	ovary
45	chr3:20143800-20152800	Weak transcription	Primary monocytes fromperipheralblood	blood
46	chr3:20144000-20147600	Enhancers	Primary T killer memory cells from peripheral blood	blood
47	chr3:20144000-20148000	Enhancers	Primary T helper naive cells from peripheral blood	blood
48	chr3:20144400-20148800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr3:20144600-20148000	Enhancers	Primary T cells fromperipheralblood	blood
50	chr3:20144600-20162000	Weak transcription	Fetal Heart	heart

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