Variant report

Variant	rs6489293
Chromosome Location	chr12:1629125-1629126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1627927..1631783-chr12:1637016..1640816,5	K562	blood:
2	chr12:1626921..1630129-chr12:1639679..1644833,6	MCF-7	breast:
3	chr12:1627927..1629732-chr12:1638277..1639813,2	K562	blood:
4	chr12:1626153..1629399-chr12:1683454..1686746,3	MCF-7	breast:
5	chr12:1626725..1629627-chr12:1683737..1685681,2	MCF-7	breast:
6	chr12:1615017..1617424-chr12:1628113..1630003,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249628	Chromatin interaction
ENSG00000111186	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10773956	0.89[AFR][1000 genomes]
rs10848505	0.82[ASN][1000 genomes]
rs10848506	0.82[ASN][1000 genomes]
rs10848507	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061811	0.82[ASN][1000 genomes]
rs11061814	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12146724	0.82[ASN][1000 genomes]
rs12304262	0.89[AFR][1000 genomes]
rs12308917	0.89[AFR][1000 genomes]
rs12368104	0.80[EUR][1000 genomes]
rs12580172	0.98[ASN][1000 genomes]
rs58860593	0.98[ASN][1000 genomes]
rs6489292	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67719042	0.82[ASN][1000 genomes]
rs7952961	0.98[ASN][1000 genomes]
rs7973400	0.82[ASN][1000 genomes]
rs7977105	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783444	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9783502	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045278	chr12:920251-1697030	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers 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 target site	46 gene(s)	inside rSNPs	diseases
2	nsv529398	chr12:941915-1741311	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv1046134	chr12:1153489-1675223	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv541344	chr12:1153489-1675223	Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	nsv1042863	chr12:1163817-1902302	Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
6	nsv541345	chr12:1163817-1902302	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
7	nsv1054178	chr12:1372157-1682699	Enhancers Strong transcription Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
8	nsv541347	chr12:1372157-1682699	Bivalent Enhancer Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
9	esv3397478	chr12:1535455-1730159	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
10	nsv1049247	chr12:1566534-1671806	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv556950	chr12:1603428-1638868	Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	nsv898584	chr12:1607390-1783251	Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
13	nsv1039629	chr12:1608565-1681391	Enhancers Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
14	nsv541349	chr12:1608565-1681391	Weak transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv898585	chr12:1611846-1674239	Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	nsv826180	chr12:1614395-1759431	Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
17	esv1808027	chr12:1618365-1645257	Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
18	esv1824458	chr12:1618365-1645257	Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
19	esv1826568	chr12:1618365-1645257	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
20	esv1836167	chr12:1618365-1645257	Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv826181	chr12:1619798-1754941	Active TSS Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
22	esv1817413	chr12:1625937-1640595	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1626000-1629400	Enhancers	NHDF-Ad	bronchial
2	chr12:1626400-1629400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr12:1626400-1629400	Enhancers	NHLF	lung
4	chr12:1627200-1629200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr12:1627200-1629200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr12:1627400-1629200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:1627400-1629200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr12:1627400-1629200	Enhancers	NH-A	brain
9	chr12:1627400-1629600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:1627600-1629200	Flanking Active TSS	Osteobl	bone
11	chr12:1627800-1629200	Enhancers	Esophagus	oesophagus
12	chr12:1627800-1629200	Enhancers	Lung	lung
13	chr12:1628000-1629200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr12:1628000-1629200	Enhancers	Fetal Intestine Small	intestine
15	chr12:1628000-1629200	Bivalent Enhancer	Fetal Stomach	stomach
16	chr12:1628000-1629200	Enhancers	Placenta Amnion	Placenta Amnion
17	chr12:1628000-1629200	Flanking Active TSS	A549	lung
18	chr12:1628000-1629400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr12:1628000-1629400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:1628200-1629200	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr12:1628200-1629200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:1628200-1629200	Enhancers	Liver	Liver
23	chr12:1628200-1629400	Flanking Active TSS	HSMMtube	muscle
24	chr12:1628400-1629200	Bivalent Enhancer	Stomach Mucosa	stomach
25	chr12:1628400-1632200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr12:1628400-1632400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:1628400-1632600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr12:1628600-1629200	Enhancers	Colonic Mucosa	Colon
29	chr12:1628600-1629200	Enhancers	Fetal Heart	heart
30	chr12:1628600-1629200	Enhancers	Rectal Mucosa Donor 29	rectum
31	chr12:1628600-1629200	Bivalent Enhancer	Stomach Smooth Muscle	stomach
32	chr12:1628600-1629400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr12:1628600-1629400	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr12:1628600-1629400	Enhancers	HepG2	liver
35	chr12:1628600-1629800	Enhancers	Breast Myoepithelial Primary Cells	Breast
36	chr12:1628600-1632200	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr12:1628800-1629400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
38	chr12:1628800-1629400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr12:1629000-1629400	Enhancers	HMEC	breast
40	chr12:1629000-1629400	Enhancers	HSMM	muscle
41	chr12:1629000-1629400	Enhancers	NHEK	skin
42	chr12:1629000-1629800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:1629000-1630200	Enhancers	Muscle Satellite Cultured Cells	--
44	chr12:1629000-1630600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr12:1629000-1632200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
46	chr12:1629000-1632200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr12:1629000-1632600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr12:1629000-1632600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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