Variant report

Variant	rs336556
Chromosome Location	chr3:161139356-161139357
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:5)
CpG islands
(count:0)
Chromatin interactive
region (count:21)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:5 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:161138544-161139400	MCF-7	breast:	n/a	n/a
2	MAX	chr3:161138482-161139472	MCF-7	breast:	n/a	n/a
3	FOXM1	chr3:161138329-161139491	MCF-7	breast:	n/a	n/a
4	HDAC2	chr3:161138334-161139534	MCF-7	breast:	n/a	chr3:161139420-161139434 chr3:161139428-161139442 chr3:161139430-161139444 chr3:161139425-161139439 chr3:161139424-161139438
5	GATA3	chr3:161137813-161139406	MCF-7	breast:	n/a	chr3:161138149-161138159 chr3:161138148-161138160 chr3:161138146-161138162 chr3:161138149-161138158

No data

(count:21 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:160821746..160823709-chr3:161138366..161141285,2	MCF-7	breast:
2	chr3:161137315..161139728-chr3:161159914..161161772,2	MCF-7	breast:
3	chr3:160954897..160957855-chr3:161138681..161140607,2	MCF-7	breast:
4	chr3:161134333..161136577-chr3:161138174..161140104,2	K562	blood:
5	chr3:160819430..160825093-chr3:161138517..161141726,6	MCF-7	breast:
6	chr3:160784766..160787646-chr3:161137298..161141604,4	MCF-7	breast:
7	chr1:197492034..197493668-chr3:161137315..161140099,2	MCF-7	breast:
8	chr3:160815084..160818315-chr3:161137399..161140050,3	MCF-7	breast:
9	chr3:161137896..161142184-chr3:161162436..161166379,4	MCF-7	breast:
10	chr3:161139196..161140956-chr3:161159538..161162067,2	MCF-7	breast:
11	chr16:2019121..2021782-chr3:161137022..161139861,2	MCF-7	breast:
12	chr3:160927027..160929410-chr3:161139082..161141538,2	MCF-7	breast:
13	chr3:161009145..161011846-chr3:161137237..161140694,4	MCF-7	breast:
14	chr3:160934874..160951087-chr3:161118055..161142485,77	MCF-7	breast:
15	chr3:161007555..161015806-chr3:161127103..161142651,19	MCF-7	breast:
16	chr3:160938218..160944428-chr3:161134456..161142008,22	MCF-7	breast:
17	chr16:28832102..28834960-chr3:161138093..161140992,2	MCF-7	breast:
18	chr3:161137822..161140079-chr3:161140327..161142102,2	MCF-7	breast:
19	chr3:160280239..160283281-chr3:161137258..161140224,3	MCF-7	breast:
20	chr3:160813203..160815910-chr3:161138848..161140414,2	MCF-7	breast:
21	chr3:161040220..161042157-chr3:161138208..161140268,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000240567	TF binding region
ENSG00000169251	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000260796	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000168488	Chromatin interaction
ENSG00000229320	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs10513566	1.00[LWK][hapmap]
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]
rs336557	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]
rs336564	1.00[LWK][hapmap];1.00[MKK][hapmap]
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:44 , 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	chr3:161134400-161139800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:161134400-161141200	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:161134400-161145200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:161134400-161148200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:161134600-161140000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr3:161137200-161141400	Enhancers	HepG2	liver
8	chr3:161137400-161139400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:161137800-161140000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr3:161138000-161139400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr3:161138000-161139400	Enhancers	Stomach Mucosa	stomach
12	chr3:161138000-161139600	Enhancers	Liver	Liver
13	chr3:161138000-161140000	Enhancers	H1 Cell Line	embryonic stem cell
14	chr3:161138000-161141400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:161138200-161139400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
16	chr3:161138200-161139400	Enhancers	HMEC	breast
17	chr3:161138200-161140000	Enhancers	Breast Myoepithelial Primary Cells	Breast
18	chr3:161138400-161139400	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
19	chr3:161138400-161139400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:161138400-161140400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:161138600-161139400	Enhancers	NH-A	brain
22	chr3:161138600-161139600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:161138600-161140600	Enhancers	Fetal Muscle Leg	muscle
24	chr3:161138800-161139400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:161138800-161139400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr3:161139000-161139400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:161139000-161139400	Enhancers	A549	lung
28	chr3:161139000-161139400	Enhancers	NHEK	skin
29	chr3:161139000-161139800	Weak transcription	Psoas Muscle	Psoas
30	chr3:161139000-161140200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
31	chr3:161139000-161140200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
32	chr3:161139000-161140200	Weak transcription	Fetal Lung	lung
33	chr3:161139000-161140400	Enhancers	H9 Cell Line	embryonic stem cell
34	chr3:161139000-161140800	Weak transcription	Fetal Brain Male	brain
35	chr3:161139200-161139400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr3:161139200-161139600	Weak transcription	NHLF	lung
37	chr3:161139200-161140200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:161139200-161140400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr3:161139200-161140400	Weak transcription	Fetal Thymus	thymus
40	chr3:161139200-161141400	Enhancers	iPS-15b Cell Line	embryonic stem cell
41	chr3:161139200-161141400	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr3:161139200-161141600	Enhancers	iPS-18 Cell Line	embryonic stem cell
43	chr3:161139200-161141800	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr3:161139200-161143600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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