Variant report

Variant	rs16928662
Chromosome Location	chr12:1815659-1815660
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1815656..1816160-chr12:1876746..1877565,2	MCF-7	breast:
2	chr12:1815296..1817227-chr12:1871744..1873347,2	MCF-7	breast:
3	chr12:1815063..1817215-chr12:1824872..1827970,3	K562	blood:
4	chr12:1797706..1801661-chr12:1812450..1816186,4	MCF-7	breast:
5	chr12:1798875..1801741-chr12:1813995..1816503,2	MCF-7	breast:
6	chr12:1814191..1816713-chr12:1818333..1820469,2	K562	blood:
7	chr12:1812993..1815717-chr12:1847079..1848811,2	K562	blood:
8	chr12:1814200..1816471-chr12:1849026..1851387,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10491959	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10848555	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061928	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061931	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061932	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061934	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061938	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061939	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11061943	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061944	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061947	0.83[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11061949	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061950	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061951	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11061953	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11061954	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11061955	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061958	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061959	1.00[CEU][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11061961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061963	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11061975	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061979	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11061980	1.00[YRI][hapmap]
rs11608456	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11610397	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11610411	1.00[CEU][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11610838	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11612238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11612414	1.00[CEU][hapmap]
rs11612726	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11613594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11614622	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12229061	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12229999	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230349	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12230994	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16928665	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2286382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2369975	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs58500393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61153802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6489322	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv832304	chr12:1710249-1868642	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats 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	24 gene(s)	inside rSNPs	diseases
4	nsv832305	chr12:1769852-1936054	Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Weak transcription Active TSS 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 target site	32 gene(s)	inside rSNPs	diseases
5	nsv948480	chr12:1776217-2284333	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
6	nsv1045312	chr12:1805856-1843202	Enhancers ZNF genes & repeats Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801000-1815800	Weak transcription	Esophagus	oesophagus
2	chr12:1801000-1815800	Weak transcription	Gastric	stomach
3	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
5	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr12:1802200-1815800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
10	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
11	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:1802400-1841200	Weak transcription	HMEC	breast
14	chr12:1803200-1815800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr12:1804400-1816000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr12:1806000-1815800	Weak transcription	Lung	lung
17	chr12:1806000-1840000	Weak transcription	Spleen	Spleen
18	chr12:1806200-1823400	Weak transcription	Dnd41	blood
19	chr12:1806200-1844400	Weak transcription	NHEK	skin
20	chr12:1806600-1815800	Weak transcription	NHDF-Ad	bronchial
21	chr12:1807200-1847400	Weak transcription	Fetal Stomach	stomach
22	chr12:1807400-1819200	Weak transcription	Primary T cells from cord blood	blood
23	chr12:1807400-1822000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:1807400-1823400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr12:1807600-1815800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr12:1807600-1815800	Weak transcription	Pancreas	Pancrea
27	chr12:1807600-1815800	Weak transcription	Sigmoid Colon	Sigmoid Colon
28	chr12:1807600-1821600	Weak transcription	Ovary	ovary
29	chr12:1807800-1817400	Weak transcription	Brain Inferior Temporal Lobe	brain
30	chr12:1808200-1820400	Weak transcription	Fetal Lung	lung
31	chr12:1808200-1820400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:1808400-1830800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
33	chr12:1808800-1815800	Weak transcription	Right Atrium	heart
34	chr12:1810600-1815800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr12:1810600-1819800	Weak transcription	Fetal Intestine Small	intestine
36	chr12:1811000-1816400	Enhancers	Liver	Liver
37	chr12:1811200-1815800	Weak transcription	Psoas Muscle	Psoas
38	chr12:1811200-1816800	Enhancers	HepG2	liver
39	chr12:1812400-1817000	Enhancers	Monocytes-CD14+_RO01746	blood
40	chr12:1812600-1817000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
41	chr12:1812600-1819400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr12:1812800-1815800	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr12:1813200-1819400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:1813200-1823400	Weak transcription	Left Ventricle	heart
45	chr12:1813400-1816400	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr12:1813400-1816600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
47	chr12:1813400-1816600	Enhancers	Stomach Mucosa	stomach
48	chr12:1813400-1816600	Enhancers	Hela-S3	cervix
49	chr12:1813400-1819200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr12:1813600-1816200	Enhancers	Duodenum Mucosa	Duodenum

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