Variant report

Variant	rs7631479
Chromosome Location	chr3:161139566-161139567
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 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:
22	chr3:161139368..161142098-chr3:161277561..161279557,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168488	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000229320	Chromatin interaction
ENSG00000271052	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000260796	Chromatin interaction

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1382427	0.88[CEU][hapmap]
rs1478565	0.88[CEU][hapmap]
rs163327	0.85[CEU][hapmap]
rs163328	0.88[CEU][hapmap]
rs189270	0.88[CEU][hapmap]
rs1993891	0.88[CEU][hapmap]
rs2004862	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs336541	0.88[CEU][hapmap]
rs336543	0.88[CEU][hapmap]
rs336567	0.92[CEU][hapmap]
rs336570	0.88[CEU][hapmap]
rs336572	0.84[CEU][hapmap]
rs336577	0.88[CEU][hapmap]
rs336580	0.83[CEU][hapmap]
rs336583	0.88[CEU][hapmap]
rs336585	0.88[CEU][hapmap]
rs336586	0.88[CEU][hapmap]
rs336589	0.87[CEU][hapmap]
rs336590	0.88[CEU][hapmap]
rs336591	0.88[CEU][hapmap]
rs336593	0.88[CEU][hapmap]
rs339101	0.92[CEU][hapmap]
rs374501	0.87[ASN][1000 genomes]
rs3849524	0.88[CEU][hapmap]
rs393076	0.87[ASN][1000 genomes]
rs4273380	0.88[CEU][hapmap]
rs4370045	0.88[CEU][hapmap]
rs4493449	0.88[CEU][hapmap]
rs456137	0.87[ASN][1000 genomes]
rs456331	0.85[ASN][1000 genomes]
rs456611	0.88[CEU][hapmap]
rs458344	0.87[ASN][1000 genomes]
rs459565	0.85[ASN][1000 genomes]
rs459592	0.87[ASN][1000 genomes]
rs4597724	0.88[CEU][hapmap]
rs459923	0.87[ASN][1000 genomes]
rs460013	0.85[ASN][1000 genomes]
rs460176	0.87[ASN][1000 genomes]
rs460508	0.88[CEU][hapmap]
rs460957	0.86[ASN][1000 genomes]
rs460987	0.85[ASN][1000 genomes]
rs463928	0.88[CEU][hapmap]
rs464766	0.88[CEU][hapmap]
rs465539	0.85[ASN][1000 genomes]
rs465964	0.87[ASN][1000 genomes]
rs466119	0.85[ASN][1000 genomes]
rs467353	0.87[ASN][1000 genomes]
rs4856705	0.92[ASN][1000 genomes]
rs6441373	0.88[CEU][hapmap]
rs6765269	0.88[CEU][hapmap]
rs6775627	0.87[CEU][hapmap]
rs6794601	0.88[CEU][hapmap]
rs7615592	0.88[CEU][hapmap]
rs7623206	0.92[CEU][hapmap]
rs7653361	0.88[CEU][hapmap]
rs9821201	0.88[CEU][hapmap]
rs9850455	0.88[CEU][hapmap]
rs9870059	0.84[CEU][hapmap]
rs9872514	0.88[CEU][hapmap]

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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7631479	NMD3	cis	parietal	SCAN
rs7631479	PPM1L	cis	cerebellum	SCAN

Chromatin state (count:36 , 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	chr3:161137800-161140000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:161138000-161139600	Enhancers	Liver	Liver
10	chr3:161138000-161140000	Enhancers	H1 Cell Line	embryonic stem cell
11	chr3:161138000-161141400	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr3:161138200-161140000	Enhancers	Breast Myoepithelial Primary Cells	Breast
13	chr3:161138400-161140400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr3:161138600-161139600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr3:161138600-161140600	Enhancers	Fetal Muscle Leg	muscle
16	chr3:161139000-161139800	Weak transcription	Psoas Muscle	Psoas
17	chr3:161139000-161140200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
18	chr3:161139000-161140200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr3:161139000-161140200	Weak transcription	Fetal Lung	lung
20	chr3:161139000-161140400	Enhancers	H9 Cell Line	embryonic stem cell
21	chr3:161139000-161140800	Weak transcription	Fetal Brain Male	brain
22	chr3:161139200-161139600	Weak transcription	NHLF	lung
23	chr3:161139200-161140200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr3:161139200-161140400	Enhancers	Pancreatic Islets	Pancreatic Islet
25	chr3:161139200-161140400	Weak transcription	Fetal Thymus	thymus
26	chr3:161139200-161141400	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:161139200-161141400	Enhancers	iPS-20b Cell Line	embryonic stem cell
28	chr3:161139200-161141600	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr3:161139200-161141800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr3:161139200-161143600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:161139400-161139800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:161139400-161140200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
33	chr3:161139400-161140200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr3:161139400-161141200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr3:161139400-161141400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr3:161139400-161141600	Enhancers	HUES48 Cell Line	embryonic stem cell

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