Variant report

Variant	rs12204124
Chromosome Location	chr6:15288663-15288664
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:164714985..164717486-chr6:15287245..15290158,2	MCF-7	breast:
2	chr6:15246208..15249749-chr6:15286361..15290108,4	K562	blood:
3	chr6:15287052..15289953-chr6:15290312..15293224,4	K562	blood:
4	chr6:15288261..15289953-chr6:15290312..15293212,2	K562	blood:
5	chr6:15274634..15276590-chr6:15288104..15290387,2	K562	blood:
6	chr6:15253215..15254764-chr6:15288126..15290824,2	K562	blood:
7	chr6:15210299..15212880-chr6:15287684..15289581,2	K562	blood:
8	chr6:15287044..15289498-chr6:15293703..15295568,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000008083	Chromatin interaction
ENSG00000235488	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10484355	1.00[CHB][hapmap]
rs10949291	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10949292	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10949294	1.00[CHB][hapmap]
rs10949295	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11759040	1.00[JPT][hapmap]
rs11759478	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs11759828	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11759847	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12192599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12198692	1.00[JPT][hapmap]
rs12198694	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12199895	0.82[CEU][hapmap];1.00[JPT][hapmap]
rs12201889	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12205420	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12206745	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209228	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs12209453	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12209539	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12209748	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12210592	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12211278	1.00[CHB][hapmap]
rs12212013	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12214719	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs12215596	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12215740	1.00[CHB][hapmap];0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13192347	1.00[CHB][hapmap]
rs13194410	1.00[CHB][hapmap]
rs13205396	1.00[CHB][hapmap]
rs16876278	1.00[CHB][hapmap]
rs17575737	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs17576233	1.00[CHB][hapmap]
rs17619730	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs17619838	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17637773	0.82[CEU][hapmap];1.00[CHB][hapmap]
rs17638192	1.00[CHB][hapmap]
rs17687211	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs17713010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28505073	0.89[EUR][1000 genomes]
rs55634912	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55980198	0.85[ASN][1000 genomes]
rs6902997	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6919296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs6935879	0.80[ASN][1000 genomes]
rs6938919	0.82[CEU][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs72834551	0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72834590	0.81[AMR][1000 genomes]
rs7765425	1.00[JPT][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv601006	chr6:15275305-15300590	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	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

No data

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:15269200-15290000	Weak transcription	NHLF	lung
2	chr6:15270200-15288800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr6:15276800-15293200	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr6:15277200-15289200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr6:15277200-15294000	Weak transcription	Fetal Muscle Leg	muscle
6	chr6:15280200-15293800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr6:15280400-15288800	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr6:15281200-15289000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr6:15281400-15289000	Weak transcription	Lung	lung
10	chr6:15281400-15293400	Weak transcription	Esophagus	oesophagus
11	chr6:15281400-15296400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr6:15281600-15294000	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:15281800-15293400	Weak transcription	Cortex derived primary cultured neurospheres	brain
14	chr6:15281800-15300200	Weak transcription	Fetal Stomach	stomach
15	chr6:15282200-15288800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr6:15282200-15289000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
17	chr6:15282200-15289200	Weak transcription	Right Atrium	heart
18	chr6:15282400-15289200	Weak transcription	Ovary	ovary
19	chr6:15282400-15299400	Weak transcription	Fetal Intestine Small	intestine
20	chr6:15282600-15290600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr6:15282600-15296400	Weak transcription	Duodenum Mucosa	Duodenum
22	chr6:15282800-15290400	Weak transcription	Fetal Kidney	kidney
23	chr6:15284600-15290200	Enhancers	Primary monocytes fromperipheralblood	blood
24	chr6:15285200-15296000	Weak transcription	Liver	Liver
25	chr6:15285200-15296400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
26	chr6:15285200-15299400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr6:15285200-15299400	Weak transcription	A549	lung
28	chr6:15285400-15288800	Weak transcription	NHDF-Ad	bronchial
29	chr6:15285400-15289000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr6:15285400-15289200	Weak transcription	Hela-S3	cervix
31	chr6:15285400-15289800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr6:15285400-15291600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr6:15285600-15289000	Weak transcription	Gastric	stomach
34	chr6:15285600-15289800	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr6:15285800-15299400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr6:15285800-15299800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr6:15286200-15288800	Weak transcription	Colon Smooth Muscle	Colon
38	chr6:15286200-15290200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
39	chr6:15286200-15296200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
40	chr6:15286400-15288800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
41	chr6:15286400-15288800	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr6:15286400-15288800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr6:15286400-15289000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr6:15286400-15289000	Weak transcription	Brain Angular Gyrus	brain
45	chr6:15286400-15289000	Weak transcription	Osteobl	bone
46	chr6:15286400-15289800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr6:15286400-15290400	Weak transcription	Fetal Lung	lung
48	chr6:15286400-15290600	Weak transcription	HMEC	breast
49	chr6:15286400-15291600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr6:15286400-15291800	Weak transcription	HSMM	muscle

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