Variant report

Variant	rs17285820
Chromosome Location	chr6:4975135-4975136
allele	A/T
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	NFIC	chr6:4974251-4975210	ECC-1	luminal epithelium:	n/a	chr6:4974924-4974941 chr6:4974925-4974941
2	NFIC	chr6:4974234-4975303	ECC-1	luminal epithelium:	n/a	chr6:4974924-4974941 chr6:4974925-4974941

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:4974594..4977196-chr6:5002682..5005673,2	MCF-7	breast:
2	chr6:4973208..4976240-chr6:4987607..4989532,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000217030	TF binding region
ENSG00000124787	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12191838	0.84[YRI][hapmap]
rs12214401	0.84[YRI][hapmap]
rs1246938	1.00[ASN][1000 genomes]
rs13197142	0.90[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17285799	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764178	0.90[CEU][hapmap]
rs34291130	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34953365	1.00[ASN][1000 genomes]
rs4959322	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
6	nsv1033905	chr6:4955826-5080904	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4973600-4975200	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr6:4973600-4975800	Enhancers	Fetal Muscle Leg	muscle
3	chr6:4973800-4975200	Enhancers	ES-I3 Cell Line	embryonic stem cell
4	chr6:4973800-4975200	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr6:4973800-4975200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:4973800-4975200	Enhancers	Adipose Nuclei	Adipose
7	chr6:4973800-4975400	Enhancers	Stomach Smooth Muscle	stomach
8	chr6:4973800-4975600	Enhancers	H1 Cell Line	embryonic stem cell
9	chr6:4973800-4975600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr6:4973800-4975600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr6:4973800-4975600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr6:4973800-4975600	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr6:4973800-4975600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr6:4973800-4975600	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr6:4973800-4975600	Enhancers	Fetal Muscle Trunk	muscle
16	chr6:4973800-4975600	Enhancers	Psoas Muscle	Psoas
17	chr6:4973800-4975800	Enhancers	Fetal Stomach	stomach
18	chr6:4974000-4975400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr6:4974000-4976000	Enhancers	Fetal Brain Male	brain
20	chr6:4974200-4975400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr6:4974200-4975600	Enhancers	Rectal Smooth Muscle	rectum
22	chr6:4974400-4975200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr6:4974400-4975600	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr6:4974600-4977200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr6:4974800-4975400	Enhancers	Colon Smooth Muscle	Colon
26	chr6:4974800-4975400	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr6:4974800-4975400	Enhancers	Skeletal Muscle Female	skeletal muscle
28	chr6:4975000-4975200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr6:4975000-4975200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr6:4975000-4975200	Enhancers	Brain Germinal Matrix	brain
31	chr6:4975000-4975200	Enhancers	Duodenum Smooth Muscle	Duodenum
32	chr6:4975000-4975400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:4975000-4975400	Enhancers	Fetal Brain Female	brain
34	chr6:4975000-4979400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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