Variant report

Variant	rs10848554
Chromosome Location	chr12:1805587-1805588
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:1801036..1802914-chr12:1804421..1806179,3	MCF-7	breast:
2	chr12:1769488..1776078-chr12:1798561..1806450,20	K562	blood:
3	chr12:1805184..1807328-chr12:1869608..1872383,2	K562	blood:
4	chr12:1770854..1772922-chr12:1803554..1806296,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000006831	Chromatin interaction
ENSG00000266043	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1058322	0.85[ASN][1000 genomes]
rs10734999	1.00[CHB][hapmap]
rs10735000	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10744548	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10744549	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10744550	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10773979	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs10773981	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10773987	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10848568	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11832522	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11836547	1.00[CHB][hapmap];0.88[JPT][hapmap]
rs12296831	0.83[EUR][1000 genomes]
rs12370189	0.85[CHB][hapmap]
rs2058112	0.83[EUR][1000 genomes]
rs4140993	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs4766414	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57216374	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60523400	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703176	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7134070	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7138701	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs7302234	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs73040720	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311218	1.00[CHB][hapmap]
rs7488369	0.93[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs767870	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7954991	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7963224	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7975375	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9805042	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9805109	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9888418	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

No data

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:1801000-1805600	Weak transcription	Pancreas	Pancrea
2	chr12:1801000-1815800	Weak transcription	Esophagus	oesophagus
3	chr12:1801000-1815800	Weak transcription	Gastric	stomach
4	chr12:1801200-1807200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr12:1801400-1806400	Weak transcription	Fetal Lung	lung
6	chr12:1801400-1806600	Weak transcription	Aorta	Aorta
7	chr12:1801600-1806000	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:1801600-1806600	Weak transcription	Fetal Brain Male	brain
9	chr12:1801600-1807600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr12:1801600-1814200	Weak transcription	HSMM	muscle
11	chr12:1801600-1815200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:1801600-1823400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr12:1801600-1827800	Weak transcription	Rectal Smooth Muscle	rectum
14	chr12:1801800-1805600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr12:1801800-1805800	Weak transcription	NHLF	lung
16	chr12:1801800-1806000	Weak transcription	Primary T cells from cord blood	blood
17	chr12:1801800-1807800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr12:1801800-1808200	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr12:1801800-1811400	Weak transcription	NH-A	brain
20	chr12:1801800-1813400	Weak transcription	A549	lung
21	chr12:1801800-1823800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr12:1801800-1828200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr12:1801800-1830800	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr12:1802200-1805600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr12:1802200-1805600	Weak transcription	Lung	lung
26	chr12:1802200-1805600	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr12:1802200-1805800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr12:1802200-1805800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:1802200-1806000	Weak transcription	Stomach Smooth Muscle	stomach
30	chr12:1802200-1806400	Weak transcription	Right Ventricle	heart
31	chr12:1802200-1806600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr12:1802200-1806600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:1802200-1806600	Weak transcription	Fetal Brain Female	brain
34	chr12:1802200-1807800	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr12:1802200-1815000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
36	chr12:1802200-1815000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:1802200-1815000	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr12:1802200-1815400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:1802200-1815800	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:1802200-1822800	Weak transcription	Thymus	Thymus
41	chr12:1802400-1805600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:1802400-1805600	Weak transcription	Left Ventricle	heart
43	chr12:1802400-1806000	Weak transcription	Fetal Stomach	stomach
44	chr12:1802400-1808800	Weak transcription	HUVEC	blood vessel
45	chr12:1802400-1811800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr12:1802400-1815000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:1802400-1822800	Weak transcription	Fetal Thymus	thymus
48	chr12:1802400-1823000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:1802400-1824600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr12:1802400-1841200	Weak transcription	HMEC	breast

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