Variant report

Variant	rs9879138
Chromosome Location	chr3:61630902-61630903
allele	A/G
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:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:61613281..61613978-chr3:61630536..61631431,2	MCF-7	breast:
2	chr3:61608730..61611507-chr3:61629104..61631590,2	MCF-7	breast:
3	chr17:56706907..56710764-chr3:61627489..61633116,12	MCF-7	breast:
4	chr3:61545829..61550428-chr3:61627610..61634098,7	MCF-7	breast:
5	chr3:61630318..61630985-chr3:61693334..61694014,2	MCF-7	breast:
6	chr17:56704810..56711827-chr3:61617461..61633126,28	MCF-7	breast:
7	chr3:61626740..61629323-chr3:61629960..61632715,2	K562	blood:
8	chr3:61630698..61632717-chr3:61639309..61641493,3	MCF-7	breast:
9	chr3:61609621..61617311-chr3:61628614..61634388,16	MCF-7	breast:
10	chr3:61626912..61632333-chr3:61647768..61651580,7	MCF-7	breast:
11	chr3:61613583..61614087-chr3:61630872..61631526,2	MCF-7	breast:
12	chr3:61546938..61548723-chr3:61630365..61632506,2	MCF-7	breast:
13	chr17:56735093..56738053-chr3:61626767..61632576,11	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000202077	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000144724	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17065131	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap]
rs17065136	1.00[ASW][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap]
rs2886527	1.00[ASW][hapmap];1.00[MEX][hapmap]
rs7610603	1.00[CEU][hapmap]
rs9812317	1.00[CEU][hapmap]
rs9843830	1.00[CEU][hapmap]
rs9870321	1.00[CEU][hapmap]
rs9878497	1.00[CEU][hapmap]

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	nsv1008615	chr3:61455419-61679037	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	esv2756995	chr3:61569557-61636156	Weak transcription Genic enhancers Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
3	esv2759153	chr3:61569557-61636156	Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
4	nsv822106	chr3:61577755-61631078	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
5	nsv1001611	chr3:61598148-61686809	Genic enhancers Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1000158	chr3:61598562-61682888	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv834712	chr3:61612540-61770232	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61616000-61633800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:61616800-61633600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:61623600-61631000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr3:61623600-61631000	Weak transcription	Fetal Lung	lung
5	chr3:61623600-61632000	Weak transcription	HUVEC	blood vessel
6	chr3:61623600-61633800	Weak transcription	Pancreas	Pancrea
7	chr3:61623800-61632400	Weak transcription	Ovary	ovary
8	chr3:61624200-61631000	Weak transcription	HSMM	muscle
9	chr3:61624200-61632400	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:61625000-61631000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:61625000-61635400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr3:61625200-61631000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr3:61626800-61633600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:61626800-61633600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr3:61627000-61633600	Weak transcription	Psoas Muscle	Psoas
16	chr3:61628000-61631000	Weak transcription	Lung	lung
17	chr3:61628000-61633600	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr3:61628200-61633600	Weak transcription	Right Ventricle	heart
19	chr3:61628400-61633600	Weak transcription	Right Atrium	heart
20	chr3:61629200-61632800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
21	chr3:61629400-61631800	Enhancers	Liver	Liver
22	chr3:61629600-61631600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr3:61629600-61636400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr3:61630000-61632000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr3:61630000-61632200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr3:61630200-61631400	Enhancers	HepG2	liver
27	chr3:61630200-61632000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
28	chr3:61630200-61632400	Weak transcription	Colon Smooth Muscle	Colon
29	chr3:61630400-61631200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr3:61630400-61631400	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
31	chr3:61630400-61631600	Enhancers	Stomach Mucosa	stomach
32	chr3:61630400-61633600	Weak transcription	Fetal Heart	heart
33	chr3:61630400-61633600	Weak transcription	Left Ventricle	heart
34	chr3:61630600-61633000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr3:61630800-61631000	Weak transcription	Sigmoid Colon	Sigmoid Colon
36	chr3:61630800-61631400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
37	chr3:61630800-61631400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
38	chr3:61630800-61631400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain

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