Variant report

Variant	rs336557
Chromosome Location	chr3:161137465-161137466
allele	C/T
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:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:161137315..161139728-chr3:161159914..161161772,2	MCF-7	breast:
2	chr3:160818575..160820574-chr3:161136841..161139242,3	MCF-7	breast:
3	chr3:160973929..160975707-chr3:161135693..161137534,2	MCF-7	breast:
4	chr3:160784766..160787646-chr3:161137298..161141604,4	MCF-7	breast:
5	chr1:197492034..197493668-chr3:161137315..161140099,2	MCF-7	breast:
6	chr3:160815084..160818315-chr3:161137399..161140050,3	MCF-7	breast:
7	chr16:2019121..2021782-chr3:161137022..161139861,2	MCF-7	breast:
8	chr3:161137228..161139292-chr3:161143191..161144767,2	MCF-7	breast:
9	chr3:161009145..161011846-chr3:161137237..161140694,4	MCF-7	breast:
10	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
11	chr3:161137133..161139067-chr6:13709956..13712143,2	MCF-7	breast:
12	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
13	chr3:160938218..160944428-chr3:161134456..161142008,22	MCF-7	breast:
14	chr3:161136644..161139076-chr3:161160623..161163367,2	MCF-7	breast:
15	chr3:160280239..160283281-chr3:161137258..161140224,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000169255	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000010017	Chromatin interaction
ENSG00000240567	Chromatin interaction
ENSG00000169251	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs163136	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs336552	0.84[ASN][1000 genomes]
rs336556	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];1.00[ASN][1000 genomes]
rs336558	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];1.00[ASN][1000 genomes]
rs336559	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];1.00[ASN][1000 genomes]
rs336560	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs336588	1.00[YRI][hapmap]
rs339111	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs339124	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs420081	0.95[ASN][1000 genomes]
rs457240	0.95[ASN][1000 genomes]
rs459679	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv533237	chr3:161019834-161804660	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	91 gene(s)	inside rSNPs	diseases
3	nsv829772	chr3:161047817-161202554	Bivalent Enhancer Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv877710	chr3:161087857-161245414	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	84 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:161131600-161140000	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr3:161134000-161138400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr3:161134400-161138400	Weak transcription	Fetal Lung	lung
4	chr3:161134400-161138600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr3:161134400-161139800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr3:161134400-161141200	Weak transcription	Brain Hippocampus Middle	brain
7	chr3:161134400-161145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:161134400-161148200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr3:161134600-161137800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr3:161134600-161138000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:161134600-161138000	Weak transcription	Liver	Liver
12	chr3:161134600-161138000	Weak transcription	Stomach Mucosa	stomach
13	chr3:161134600-161138000	Weak transcription	A549	lung
14	chr3:161134600-161138200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr3:161134600-161138200	Weak transcription	NHEK	skin
16	chr3:161134600-161138600	Weak transcription	HUVEC	blood vessel
17	chr3:161134600-161138600	Weak transcription	NH-A	brain
18	chr3:161134600-161138600	Weak transcription	NHLF	lung
19	chr3:161134600-161138800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr3:161134600-161138800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr3:161134600-161140000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr3:161134800-161138000	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:161137200-161138000	Enhancers	H9 Cell Line	embryonic stem cell
24	chr3:161137200-161141400	Enhancers	HepG2	liver
25	chr3:161137400-161137600	Enhancers	H1 Cell Line	embryonic stem cell
26	chr3:161137400-161138000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr3:161137400-161138200	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr3:161137400-161138400	Enhancers	HUES6 Cell Line	embryonic stem cell
29	chr3:161137400-161138400	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:161137400-161138800	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr3:161137400-161139400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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