Variant report

Variant	rs2306011
Chromosome Location	chr6:56821191-56821192
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr6:56819958-56821217	MCF10A-Er-Src	breast:	n/a	chr6:56820510-56820519
2	MXI1	chr6:56817851-56821832	SK-N-SH	brain:	n/a	chr6:56820811-56820820 chr6:56819810-56819819
3	RAD21	chr6:56819769-56821201	HCT-116	colon:	n/a	chr6:56819858-56819872
4	CTCF	chr6:56818870-56821806	SK-N-SH	brain:	n/a	chr6:56820848-56820864 chr6:56819859-56819872 chr6:56819852-56819865 chr6:56819999-56820012 chr6:56819856-56819874

No.	Distal block	Cell Line	Cell type
1	chr6:56818015..56821855-chr6:57180367..57183028,4	K562	blood:
2	chr6:56817930..56821539-chr6:56909452..56912838,6	K562	blood:
3	chr6:56816669..56821714-chr6:56908406..56912975,10	K562	blood:
4	chr6:56820475..56822704-chr6:56829156..56832250,3	MCF-7	breast:
5	chr6:56820330..56821970-chr6:56922226..56924549,2	MCF-7	breast:
6	chr6:56767464..56768319-chr6:56820397..56821373,5	MCF-7	breast:
7	chr6:56818533..56822842-chr6:56954657..56959004,6	K562	blood:
8	chr6:56818562..56821573-chr6:56964600..56969072,4	K562	blood:
9	chr6:56714424..56718313-chr6:56818301..56821248,4	MCF-7	breast:
10	chr6:56820267..56822074-chr6:56879367..56881411,2	K562	blood:

Variant related genes	Relation type
DST	TF binding region
ENSG00000146143	Chromatin interaction
ENSG00000151914	Chromatin interaction
ENSG00000112200	Chromatin interaction
ENSG00000168116	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1007417	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1016048	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10498814	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs12175661	0.96[EUR][1000 genomes]
rs13205191	0.96[EUR][1000 genomes]
rs1597694	0.96[ASN][1000 genomes]
rs16888268	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17685356	0.96[ASN][1000 genomes]
rs17758527	0.96[EUR][1000 genomes]
rs17758663	1.00[CEU][hapmap];1.00[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];0.97[ASN][1000 genomes]
rs1839837	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2006930	0.96[ASN][1000 genomes]
rs2008698	0.97[ASN][1000 genomes]
rs28498151	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34589109	0.93[ASN][1000 genomes]
rs34703235	0.97[ASN][1000 genomes]
rs34896907	0.94[ASN][1000 genomes]
rs35553446	0.97[ASN][1000 genomes]
rs4576249	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs57994994	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58099889	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58332182	0.88[EUR][1000 genomes]
rs59106338	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs60401134	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60910121	0.92[EUR][1000 genomes]
rs62411412	0.88[EUR][1000 genomes]
rs62411417	0.92[EUR][1000 genomes]
rs62411418	0.92[EUR][1000 genomes]
rs62411419	0.92[EUR][1000 genomes]
rs62411420	0.96[EUR][1000 genomes]
rs62411421	0.96[EUR][1000 genomes]
rs62411422	0.96[EUR][1000 genomes]
rs62411423	0.96[EUR][1000 genomes]
rs62411425	0.96[EUR][1000 genomes]
rs62411430	0.96[EUR][1000 genomes]
rs62417377	0.96[EUR][1000 genomes]
rs62417378	0.94[EUR][1000 genomes]
rs62417384	0.97[ASN][1000 genomes]
rs62417385	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62417410	0.96[ASN][1000 genomes]
rs6901192	0.81[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs6901660	0.96[ASN][1000 genomes]
rs6904172	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs6915492	0.96[ASN][1000 genomes]
rs6924882	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6935636	0.96[ASN][1000 genomes]
rs720885	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7760435	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9349842	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9357936	0.96[EUR][1000 genomes]
rs9367700	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367701	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9367702	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370550	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9370552	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9370553	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9370554	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382669	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9382670	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9382673	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9382674	0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs9382675	0.96[ASN][1000 genomes]
rs9396238	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9396240	1.00[CEU][hapmap];1.00[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];0.97[ASN][1000 genomes]
rs9396245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9396249	0.96[ASN][1000 genomes]
rs9396251	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9396252	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap]
rs9396254	0.96[EUR][1000 genomes]
rs9464411	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9464412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9464413	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475757	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9475758	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9475760	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9475761	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9475762	1.00[CEU][hapmap];1.00[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];0.97[ASN][1000 genomes]
rs9475763	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[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	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1022714	chr6:56729767-56826642	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv538229	chr6:56729767-56826642	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56817800-56821200	Active TSS	NHDF-Ad	bronchial
2	chr6:56818000-56821200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr6:56818000-56821400	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr6:56818400-56821200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:56818400-56821800	Active TSS	Brain Inferior Temporal Lobe	brain
6	chr6:56818600-56821200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
7	chr6:56818600-56821200	Active TSS	K562	blood
8	chr6:56818600-56821400	Active TSS	Brain Anterior Caudate	brain
9	chr6:56818600-56821800	Active TSS	Brain Angular Gyrus	brain
10	chr6:56819000-56821200	Active TSS	Fetal Brain Female	brain
11	chr6:56819200-56821200	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr6:56819400-56821200	Active TSS	ES-I3 Cell Line	embryonic stem cell
13	chr6:56819400-56821200	Active TSS	H1 Cell Line	embryonic stem cell
14	chr6:56819400-56821200	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr6:56819400-56821200	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr6:56820200-56821200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr6:56820200-56821200	Bivalent Enhancer	Fetal Brain Male	brain
18	chr6:56820200-56821200	Flanking Active TSS	HMEC	breast
19	chr6:56820200-56821400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr6:56820200-56821400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr6:56820200-56821600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr6:56820400-56821200	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:56820400-56821400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:56820400-56821400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr6:56820400-56821600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr6:56820600-56821200	Flanking Active TSS	NHEK	skin
27	chr6:56820600-56821600	Flanking Active TSS	NHLF	lung
28	chr6:56820800-56821200	Bivalent Enhancer	Primary T cells from cord blood	blood
29	chr6:56820800-56821600	Enhancers	Brain Substantia Nigra	brain
30	chr6:56820800-56822400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr6:56821000-56821200	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
32	chr6:56821000-56821200	Enhancers	Primary hematopoietic stem cells	blood
33	chr6:56821000-56821200	Bivalent Enhancer	Fetal Kidney	kidney
34	chr6:56821000-56821200	Flanking Active TSS	A549	lung
35	chr6:56821000-56821200	Active TSS	NH-A	brain
36	chr6:56821000-56821400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr6:56821000-56821400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr6:56821000-56821400	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
39	chr6:56821000-56821400	Flanking Bivalent TSS/Enh	HUES64 Cell Line	embryonic stem cell
40	chr6:56821000-56821400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr6:56821000-56821400	Enhancers	Muscle Satellite Cultured Cells	--
42	chr6:56821000-56821400	Enhancers	Cortex derived primary cultured neurospheres	brain
43	chr6:56821000-56821400	Enhancers	Brain Cingulate Gyrus	brain
44	chr6:56821000-56821400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr6:56821000-56821400	Flanking Active TSS	GM12878-XiMat	blood
46	chr6:56821000-56821400	Bivalent Enhancer	HepG2	liver
47	chr6:56821000-56821600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr6:56821000-56821600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr6:56821000-56821600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr6:56821000-56821600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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