Variant report

Variant	rs4390920
Chromosome Location	chr3:61612245-61612246
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: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	chr19:42756346..42758374-chr3:61612171..61614717,2	MCF-7	breast:
2	chr3:61609621..61617311-chr3:61628614..61634388,16	MCF-7	breast:
3	chr17:56671169..56673208-chr3:61611941..61613573,2	MCF-7	breast:
4	chr17:56649570..56655387-chr3:61609668..61616460,11	MCF-7	breast:
5	chr3:61611728..61614582-chr3:61688130..61691017,3	MCF-7	breast:
6	chr17:56730838..56733120-chr3:61609560..61612509,2	MCF-7	breast:
7	chr17:56726675..56729447-chr3:61611822..61614442,2	MCF-7	breast:
8	chr17:56734668..56738970-chr3:61603973..61616839,24	MCF-7	breast:
9	chr17:57922105..57925001-chr3:61610835..61613276,2	MCF-7	breast:
10	chr17:56635071..56649233-chr3:61603708..61615718,44	MCF-7	breast:
11	chr17:56707443..56710525-chr3:61604154..61615875,21	MCF-7	breast:
12	chr17:56703125..56711935-chr3:61611656..61626888,27	MCF-7	breast:
13	chr17:56735102..56739393-chr3:61610159..61616019,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000105722	Chromatin interaction
ENSG00000121101	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000266826	Chromatin interaction
ENSG00000201524	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs56696131	1.00[AMR][1000 genomes]
rs56917130	0.92[AFR][1000 genomes]
rs57484041	0.93[AFR][1000 genomes]
rs57490914	0.92[AFR][1000 genomes]
rs57929835	0.93[AFR][1000 genomes]
rs57943064	1.00[AMR][1000 genomes]
rs57953857	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58325144	0.95[AFR][1000 genomes]
rs58814661	1.00[AMR][1000 genomes]
rs59639668	0.87[AFR][1000 genomes]
rs59716534	0.95[AFR][1000 genomes]
rs60197600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60197976	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60473152	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6801604	1.00[AMR][1000 genomes]
rs6805288	1.00[AMR][1000 genomes]
rs72874738	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72874741	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72874744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72874746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72874749	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72874755	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72888670	1.00[AMR][1000 genomes]
rs72888675	1.00[AMR][1000 genomes]
rs72888676	1.00[AMR][1000 genomes]
rs72888678	1.00[AMR][1000 genomes]
rs72890425	0.93[AFR][1000 genomes]
rs7637818	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs7640772	1.00[AMR][1000 genomes]
rs9878497	1.00[MEX][hapmap]
rs9878929	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834711	chr3:61413762-61612539	Flanking Active TSS Enhancers Genic enhancers Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	esv35004	chr3:61570149-61626426	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	11 gene(s)	inside rSNPs	diseases
6	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
7	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
8	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
9	esv1800730	chr3:61599495-61620573	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Active TSS	Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
10	esv3463358	chr3:61610515-61615945	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
11	esv3463359	chr3:61610515-61615945	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers	Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61581400-61613400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr3:61586400-61614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:61592800-61619800	Weak transcription	Fetal Muscle Trunk	muscle
4	chr3:61598800-61623200	Weak transcription	Aorta	Aorta
5	chr3:61602800-61613200	Weak transcription	NH-A	brain
6	chr3:61603000-61613600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr3:61603000-61613600	Weak transcription	Right Ventricle	heart
8	chr3:61603000-61614200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr3:61603000-61620000	Weak transcription	Left Ventricle	heart
10	chr3:61603200-61613000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:61603200-61613200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:61603200-61623400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr3:61603400-61613400	Weak transcription	Fetal Lung	lung
14	chr3:61603400-61613400	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr3:61603400-61613600	Weak transcription	Fetal Kidney	kidney
16	chr3:61603400-61615400	Weak transcription	HSMMtube	muscle
17	chr3:61603400-61620400	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr3:61603400-61622600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr3:61603600-61622800	Weak transcription	Ovary	ovary
20	chr3:61607600-61612400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:61609600-61612400	Weak transcription	Fetal Heart	heart
22	chr3:61609800-61612600	Weak transcription	HSMM	muscle
23	chr3:61609800-61613000	Weak transcription	NHEK	skin
24	chr3:61610200-61612400	Weak transcription	Fetal Intestine Large	intestine
25	chr3:61610200-61613800	Enhancers	iPS-18 Cell Line	embryonic stem cell
26	chr3:61610200-61615800	Enhancers	iPS-15b Cell Line	embryonic stem cell
27	chr3:61610400-61613200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:61610600-61612600	Enhancers	H1 Cell Line	embryonic stem cell
29	chr3:61610600-61612600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr3:61610600-61613600	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:61610600-61613800	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr3:61610600-61613800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr3:61610800-61613800	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr3:61611200-61613600	Enhancers	ES-I3 Cell Line	embryonic stem cell
35	chr3:61611200-61615800	Enhancers	iPS-20b Cell Line	embryonic stem cell
36	chr3:61611400-61613600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr3:61611400-61614400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
38	chr3:61611400-61616400	Enhancers	HepG2	liver
39	chr3:61611800-61612600	Enhancers	Psoas Muscle	Psoas
40	chr3:61611800-61615200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr3:61612000-61612600	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr3:61612000-61613800	Enhancers	Colon Smooth Muscle	Colon
43	chr3:61612000-61616200	Enhancers	HUES6 Cell Line	embryonic stem cell
44	chr3:61612000-61625600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr3:61612200-61612400	Enhancers	Cortex derived primary cultured neurospheres	brain
46	chr3:61612200-61612400	Enhancers	Lung	lung
47	chr3:61612200-61612400	Enhancers	Pancreas	Pancrea
48	chr3:61612200-61612400	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr3:61612200-61612600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
50	chr3:61612200-61612600	Flanking Active TSS	Liver	Liver

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