Variant report

Variant	rs12209228
Chromosome Location	chr6:15320796-15320797
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:15197204..15198861-chr6:15320773..15322728,2	MCF-7	breast:
2	chr6:15209912..15212798-chr6:15319363..15322301,3	K562	blood:
3	chr6:15320114..15322531-chr6:15458945..15460458,2	MCF-7	breast:
4	chr6:15294357..15295870-chr6:15319327..15321466,2	K562	blood:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10949291	0.95[ASN][1000 genomes]
rs10949292	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10949293	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10949294	1.00[CHB][hapmap]
rs10949295	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11759040	1.00[JPT][hapmap]
rs11759478	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs11759828	0.90[ASN][1000 genomes]
rs11759847	0.90[ASN][1000 genomes]
rs12192599	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12198692	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs12198694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12199895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12201889	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12204124	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12205420	0.90[ASN][1000 genomes]
rs12206745	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs12209453	0.90[ASN][1000 genomes]
rs12209539	0.95[ASN][1000 genomes]
rs12209748	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210592	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12211278	1.00[CHB][hapmap]
rs12212013	1.00[ASN][1000 genomes]
rs12214719	0.92[EUR][1000 genomes]
rs12215596	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12215740	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13192347	1.00[CHB][hapmap]
rs13194410	1.00[CHB][hapmap]
rs13205396	1.00[CHB][hapmap]
rs13205612	1.00[CHB][hapmap]
rs16876278	1.00[CHB][hapmap]
rs17575737	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17576233	1.00[CHB][hapmap]
rs17576436	1.00[CHB][hapmap]
rs17619730	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs17619838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17637773	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs17638192	1.00[CHB][hapmap]
rs17687211	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17713010	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs55634912	1.00[ASN][1000 genomes]
rs55980198	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6902997	0.90[ASN][1000 genomes]
rs6919296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6935879	0.81[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6938919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72834551	0.95[ASN][1000 genomes]
rs72834590	0.83[ASN][1000 genomes]
rs7765425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027010	chr6:15201803-15425629	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv538140	chr6:15217899-15547127	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv1030558	chr6:15234675-15449137	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv538141	chr6:15234675-15509163	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
5	nsv538142	chr6:15243960-15404893	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
6	nsv949448	chr6:15279490-15449441	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1025512	chr6:15291551-15452395	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	nsv538143	chr6:15291551-15452395	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	nsv538144	chr6:15310696-15364984	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15311000-15322200	Weak transcription	Fetal Intestine Small	intestine
2	chr6:15311200-15330600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr6:15313200-15322400	Weak transcription	HMEC	breast
4	chr6:15313200-15322800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr6:15313200-15323400	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr6:15313200-15326600	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr6:15313400-15322600	Weak transcription	Osteobl	bone
8	chr6:15313600-15322800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr6:15313800-15321000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr6:15313800-15321000	Weak transcription	NHEK	skin
11	chr6:15313800-15321200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:15313800-15325400	Weak transcription	Liver	Liver
13	chr6:15314000-15322000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr6:15314000-15322400	Weak transcription	Gastric	stomach
15	chr6:15314000-15323800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr6:15314200-15324000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr6:15314200-15326600	Weak transcription	Ovary	ovary
18	chr6:15314400-15322200	Weak transcription	Pancreas	Pancrea
19	chr6:15314400-15327600	Weak transcription	Aorta	Aorta
20	chr6:15314600-15322600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:15315000-15322600	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr6:15315400-15323200	Enhancers	iPS-18 Cell Line	embryonic stem cell
23	chr6:15315600-15321200	Enhancers	Primary T helper cells fromperipheralblood	blood
24	chr6:15315600-15321400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
25	chr6:15315600-15323400	Enhancers	HUES48 Cell Line	embryonic stem cell
26	chr6:15316000-15321200	Enhancers	H1 Cell Line	embryonic stem cell
27	chr6:15316600-15322400	Enhancers	HUES6 Cell Line	embryonic stem cell
28	chr6:15316800-15321400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
29	chr6:15317000-15321200	Flanking Active TSS	GM12878-XiMat	blood
30	chr6:15317200-15321600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr6:15317200-15323600	Enhancers	Primary hematopoietic stem cells	blood
32	chr6:15317400-15321200	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr6:15317400-15323600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr6:15317800-15322200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:15317800-15322200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr6:15318000-15321000	Enhancers	Monocytes-CD14+_RO01746	blood
37	chr6:15318000-15323800	Enhancers	K562	blood
38	chr6:15318200-15323600	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:15318200-15326600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr6:15318400-15322200	Weak transcription	Stomach Mucosa	stomach
41	chr6:15318600-15322800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
42	chr6:15318600-15326400	Weak transcription	Spleen	Spleen
43	chr6:15318800-15323000	Weak transcription	Stomach Smooth Muscle	stomach
44	chr6:15318800-15323800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr6:15319000-15320800	Weak transcription	NHLF	lung
46	chr6:15319000-15322200	Weak transcription	Duodenum Mucosa	Duodenum
47	chr6:15319000-15322200	Weak transcription	Small Intestine	intestine
48	chr6:15319000-15322400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr6:15319000-15322800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:15319000-15323200	Weak transcription	Esophagus	oesophagus

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