Variant report

Variant	rs12490215
Chromosome Location	chr3:20156185-20156186
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	chr3:19987552..19989415-chr3:20155282..20158002,2	MCF-7	breast:
2	chr3:20154687..20157429-chr3:20160845..20162920,2	K562	blood:

Variant related genes	Relation type
ENSG00000163576	Chromatin interaction
ENSG00000144566	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10084714	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1061636	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1124376	0.95[EUR][1000 genomes]
rs11712709	0.98[EUR][1000 genomes]
rs12488369	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12488589	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17006610	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17006623	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17797343	1.00[ASN][1000 genomes]
rs28716666	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34159701	1.00[ASN][1000 genomes]
rs3828352	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41285057	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4417886	0.95[EUR][1000 genomes]
rs56042248	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56117426	0.81[EUR][1000 genomes]
rs61138004	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61457790	0.98[EUR][1000 genomes]
rs62241674	1.00[ASN][1000 genomes]
rs62241698	1.00[ASN][1000 genomes]
rs62243080	0.81[EUR][1000 genomes]
rs62243081	0.81[EUR][1000 genomes]
rs62243098	0.95[EUR][1000 genomes]
rs62243100	0.96[EUR][1000 genomes]
rs62243131	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6550307	0.82[EUR][1000 genomes]
rs67660889	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67713322	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771367	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6774367	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791385	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6793985	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6807771	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7618597	0.95[EUR][1000 genomes]
rs7639282	0.96[EUR][1000 genomes]
rs9819628	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9819739	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9828701	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9836418	0.82[EUR][1000 genomes]
rs9852109	1.00[ASN][1000 genomes]
rs9855900	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9857135	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 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	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
16	esv3394910	chr3:20150394-20203576	Weak transcription Genic enhancers Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
17	esv3334928	chr3:20150414-20203546	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
18	esv1832674	chr3:20152772-20605302	Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Weak transcription 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	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:20116400-20194800	Weak transcription	NHDF-Ad	bronchial
2	chr3:20128200-20175800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:20135200-20173800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr3:20137400-20156600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr3:20138800-20156400	Weak transcription	Rectal Smooth Muscle	rectum
6	chr3:20139000-20164000	Weak transcription	Small Intestine	intestine
7	chr3:20139800-20161000	Weak transcription	Fetal Intestine Small	intestine
8	chr3:20141200-20167400	Weak transcription	HSMMtube	muscle
9	chr3:20141200-20222400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr3:20142600-20189400	Weak transcription	Fetal Brain Male	brain
11	chr3:20144600-20162000	Weak transcription	Fetal Heart	heart
12	chr3:20146000-20156400	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:20146000-20156400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr3:20146200-20156400	Weak transcription	Brain Angular Gyrus	brain
15	chr3:20146400-20157600	Weak transcription	Fetal Brain Female	brain
16	chr3:20146400-20163400	Weak transcription	Brain Germinal Matrix	brain
17	chr3:20147400-20169600	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr3:20147600-20156200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr3:20147600-20194200	Weak transcription	Dnd41	blood
20	chr3:20148000-20167000	Weak transcription	GM12878-XiMat	blood
21	chr3:20148800-20159200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:20150000-20159800	Strong transcription	Primary T cells from cord blood	blood
23	chr3:20150200-20158600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr3:20150600-20156400	Weak transcription	K562	blood
25	chr3:20150800-20159400	Strong transcription	Fetal Thymus	thymus
26	chr3:20150800-20166200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr3:20151000-20196800	Weak transcription	Stomach Mucosa	stomach
28	chr3:20151200-20159800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr3:20151200-20179000	Weak transcription	Fetal Kidney	kidney
30	chr3:20151600-20158800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr3:20151600-20175800	Strong transcription	Primary T helper cells fromperipheralblood	blood
32	chr3:20152000-20182800	Weak transcription	Colonic Mucosa	Colon
33	chr3:20152200-20162600	Strong transcription	Thymus	Thymus
34	chr3:20152400-20159400	Strong transcription	Stomach Smooth Muscle	stomach
35	chr3:20152400-20162600	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr3:20152600-20159200	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr3:20152600-20159600	Strong transcription	Primary B cells from peripheral blood	blood
38	chr3:20152600-20175200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr3:20152800-20156800	Strong transcription	Skeletal Muscle Male	skeletal muscle
40	chr3:20152800-20157200	Strong transcription	Fetal Intestine Large	intestine
41	chr3:20152800-20159200	Strong transcription	Primary monocytes fromperipheralblood	blood
42	chr3:20152800-20159200	Strong transcription	Liver	Liver
43	chr3:20152800-20159400	Strong transcription	Primary neutrophils fromperipheralblood	blood
44	chr3:20152800-20170200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr3:20152800-20175000	Strong transcription	Primary T cells fromperipheralblood	blood
46	chr3:20152800-20176200	Strong transcription	Primary T helper cells PMA-I stimulated	--
47	chr3:20153000-20157200	Strong transcription	Brain Hippocampus Middle	brain
48	chr3:20153000-20159200	Strong transcription	Fetal Lung	lung
49	chr3:20153000-20159400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr3:20153000-20159400	Strong transcription	Adipose Nuclei	Adipose

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