Variant report

Variant	rs2452580
Chromosome Location	chr4:95465526-95465527
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:95464708..95469426-chr4:95470140..95474023,5	K562	blood:
2	chr4:95372608..95374440-chr4:95464990..95467964,2	MCF-7	breast:
3	chr4:95458379..95460078-chr4:95465243..95467289,2	K562	blood:
4	chr4:95460565..95462692-chr4:95465018..95467575,2	K562	blood:
5	chr4:95372341..95373893-chr4:95463516..95466280,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000163110	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10019142	0.83[ASN][1000 genomes]
rs10033326	0.91[CHB][hapmap]
rs10034824	0.94[CHB][hapmap]
rs1032420	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12500426	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs12639623	0.90[CHB][hapmap]
rs12639887	0.85[CHB][hapmap]
rs12642449	0.86[CHB][hapmap]
rs12645971	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13110115	0.96[CEU][hapmap];0.90[CHB][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13122786	0.86[CHB][hapmap]
rs13143502	0.96[CEU][hapmap];0.89[CHB][hapmap];0.83[JPT][hapmap];0.85[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs13146878	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1493112	0.82[CHB][hapmap]
rs1972011	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452008	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452010	0.88[CEU][hapmap];0.90[CHB][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2452563	0.80[CEU][hapmap]
rs2452569	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2452570	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2452571	1.00[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2452572	0.85[ASN][1000 genomes]
rs2452574	0.85[CEU][hapmap];0.90[CHB][hapmap];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2452575	0.92[CEU][hapmap];0.90[CHB][hapmap];0.80[ASN][1000 genomes]
rs2452578	0.80[CHB][hapmap]
rs2452582	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452584	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452585	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452586	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2452589	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2452601	0.86[CHB][hapmap]
rs2510769	0.91[CHB][hapmap]
rs2510772	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510774	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2510775	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2510776	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510777	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2510779	0.84[ASN][1000 genomes]
rs2510780	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2510781	0.88[CEU][hapmap];0.90[CHB][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28740868	0.86[ASN][1000 genomes]
rs3792666	0.96[CEU][hapmap];0.89[CHB][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3805263	0.90[CHB][hapmap]
rs3805266	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs3805285	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3843444	0.95[CHB][hapmap];0.82[JPT][hapmap]
rs4634230	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4699505	0.92[CEU][hapmap];0.90[CHB][hapmap];0.82[JPT][hapmap]
rs5013417	0.81[CHB][hapmap]
rs6854173	0.91[CHB][hapmap]
rs7662466	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs766520	0.84[CEU][hapmap]
rs902981	0.91[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv993495	chr4:94992315-95482578	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv594901	chr4:95254730-95493246	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv1003743	chr4:95255957-95469831	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:95422400-95482800	Weak transcription	Fetal Muscle Trunk	muscle
2	chr4:95442000-95469600	Weak transcription	Primary T cells from cord blood	blood
3	chr4:95449200-95470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr4:95450400-95465800	Weak transcription	Lung	lung
5	chr4:95456800-95469800	Weak transcription	Ovary	ovary
6	chr4:95456800-95470200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr4:95457000-95469800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr4:95457400-95465800	Weak transcription	Pancreas	Pancrea
9	chr4:95457400-95469800	Weak transcription	Fetal Muscle Leg	muscle
10	chr4:95457400-95470000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr4:95457400-95485400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:95457600-95465600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr4:95457800-95466400	Weak transcription	Brain Substantia Nigra	brain
14	chr4:95458000-95469800	Weak transcription	Small Intestine	intestine
15	chr4:95458000-95480400	Weak transcription	Brain Hippocampus Middle	brain
16	chr4:95458200-95465600	Weak transcription	NHLF	lung
17	chr4:95458200-95483000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr4:95458200-95488800	Weak transcription	Stomach Smooth Muscle	stomach
19	chr4:95458400-95468600	Weak transcription	Liver	Liver
20	chr4:95458400-95469800	Weak transcription	Fetal Intestine Large	intestine
21	chr4:95459000-95473000	Weak transcription	Fetal Kidney	kidney
22	chr4:95459000-95480400	Weak transcription	Adipose Nuclei	Adipose
23	chr4:95459600-95471000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr4:95459800-95466400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:95459800-95481200	Weak transcription	Aorta	Aorta
26	chr4:95460000-95466000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr4:95460200-95472400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr4:95460400-95465600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr4:95460400-95469800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr4:95462200-95466400	Weak transcription	Rectal Smooth Muscle	rectum
31	chr4:95462200-95468400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr4:95462400-95466000	Weak transcription	K562	blood
33	chr4:95462600-95470200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr4:95462800-95465600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr4:95462800-95465600	Weak transcription	HSMMtube	muscle
36	chr4:95463000-95465800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr4:95463000-95466000	Weak transcription	Placenta Amnion	Placenta Amnion
38	chr4:95463000-95468400	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr4:95463000-95469600	Weak transcription	HUES48 Cell Line	embryonic stem cell
40	chr4:95463000-95469600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr4:95463000-95480400	Weak transcription	Right Ventricle	heart
42	chr4:95463000-95487800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr4:95463200-95465600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr4:95463200-95470000	Weak transcription	Fetal Intestine Small	intestine
45	chr4:95463200-95481200	Weak transcription	Left Ventricle	heart
46	chr4:95464600-95466000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:95464800-95466000	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr4:95464800-95467600	Enhancers	Fetal Heart	heart
49	chr4:95465000-95467600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr4:95465200-95465600	Genic enhancers	Osteobl	bone

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