Variant report

Variant	rs3807580
Chromosome Location	chr7:5707499-5707500
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:5705184..5710159-chr7:5710704..5713779,6	K562	blood:
2	chr7:5702659..5705852-chr7:5707033..5711502,4	K562	blood:
3	chr7:5706003..5708610-chr7:5751517..5753079,2	K562	blood:
4	chr7:5707494..5709701-chr7:5721366..5724112,2	MCF-7	breast:
5	chr7:5705408..5708963-chr7:5711665..5713452,3	K562	blood:

Variant related genes	Relation type
ENSG00000011275	Chromatin interaction

Extended variants
information (count: 64 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10241310	0.86[JPT][hapmap]
rs2287593	0.88[JPT][hapmap]
rs2287595	0.88[JPT][hapmap];1.00[MEX][hapmap]
rs2345938	0.95[ASN][1000 genomes]
rs28519438	0.84[ASN][1000 genomes]
rs35780366	0.85[AMR][1000 genomes]
rs3801012	1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3807575	0.85[AMR][1000 genomes]
rs4720640	0.86[JPT][hapmap]
rs57309152	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58364611	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs58503972	0.80[EUR][1000 genomes]
rs59987579	0.85[AMR][1000 genomes]
rs60181616	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60372872	0.84[ASN][1000 genomes]
rs60442234	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60889993	0.85[AMR][1000 genomes]
rs61033429	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61210914	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61260366	1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6463507	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs6463513	0.84[ASN][1000 genomes]
rs6944627	0.84[ASN][1000 genomes]
rs6951438	0.95[ASN][1000 genomes]
rs6956564	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6959871	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs6960381	0.88[JPT][hapmap]
rs6969585	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6971289	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes]
rs73339903	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73341604	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7795879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7804319	0.88[JPT][hapmap];0.89[AMR][1000 genomes]
rs7806110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7809733	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs852265	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs852266	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs852375	1.00[MEX][hapmap]
rs852376	1.00[MEX][hapmap]
rs852397	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs852402	0.88[JPT][hapmap];0.88[MEX][hapmap]
rs852410	0.88[JPT][hapmap]
rs852415	0.88[JPT][hapmap]
rs852441	1.00[MEX][hapmap]
rs852516	1.00[MEX][hapmap]
rs8772	0.81[AMR][1000 genomes]
rs9648579	1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9691118	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869165	chr7:4889618-5799719	Weak transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	352 gene(s)	inside rSNPs	diseases
2	nsv530979	chr7:5101631-5864814	Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	350 gene(s)	inside rSNPs	diseases
3	nsv530981	chr7:5157150-5920006	Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	348 gene(s)	inside rSNPs	diseases
4	nsv530983	chr7:5370746-6070852	Active TSS Strong transcription Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	368 gene(s)	inside rSNPs	diseases
5	nsv916391	chr7:5417945-5889565	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	336 gene(s)	inside rSNPs	diseases
6	nsv533108	chr7:5488018-6316581	Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	390 gene(s)	inside rSNPs	diseases
7	nsv482449	chr7:5557585-5743673	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	294 gene(s)	inside rSNPs	diseases
8	nsv1033556	chr7:5565080-6186815	Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
9	nsv538710	chr7:5565080-6186815	Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	357 gene(s)	inside rSNPs	diseases
10	nsv530467	chr7:5617816-5815082	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
11	nsv1017612	chr7:5629728-5819144	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
12	nsv1021989	chr7:5629728-6186815	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
13	nsv887417	chr7:5667645-5760860	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
14	nsv887418	chr7:5675305-5772551	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
15	nsv887419	chr7:5703669-5820383	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
16	nsv1028652	chr7:5706207-5769489	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:5674800-5728200	Weak transcription	Small Intestine	intestine
2	chr7:5683600-5710400	Weak transcription	Colonic Mucosa	Colon
3	chr7:5691000-5712000	Weak transcription	Fetal Kidney	kidney
4	chr7:5691200-5721000	Weak transcription	Pancreas	Pancrea
5	chr7:5692600-5717400	Weak transcription	Hela-S3	cervix
6	chr7:5699200-5723000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr7:5702000-5717600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr7:5702000-5730600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr7:5702400-5708600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr7:5702400-5710400	Weak transcription	NHEK	skin
11	chr7:5702400-5712600	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr7:5702400-5717000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr7:5702400-5721400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr7:5702600-5708200	Weak transcription	NH-A	brain
15	chr7:5702600-5710400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr7:5702600-5711600	Weak transcription	Right Atrium	heart
17	chr7:5702600-5717200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
18	chr7:5702600-5717200	Weak transcription	Aorta	Aorta
19	chr7:5702600-5717400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
20	chr7:5702600-5717600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr7:5702600-5718000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr7:5702800-5708400	Weak transcription	GM12878-XiMat	blood
23	chr7:5702800-5708600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr7:5702800-5709800	Weak transcription	Lung	lung
25	chr7:5702800-5710200	Weak transcription	NHLF	lung
26	chr7:5702800-5710400	Weak transcription	Brain Anterior Caudate	brain
27	chr7:5702800-5710400	Weak transcription	Brain Germinal Matrix	brain
28	chr7:5702800-5710800	Weak transcription	Brain Angular Gyrus	brain
29	chr7:5702800-5712400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr7:5702800-5712600	Weak transcription	Esophagus	oesophagus
31	chr7:5702800-5716200	Weak transcription	HSMM	muscle
32	chr7:5702800-5716800	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr7:5702800-5727200	Weak transcription	Psoas Muscle	Psoas
34	chr7:5703000-5707600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr7:5703000-5708600	Weak transcription	Duodenum Mucosa	Duodenum
36	chr7:5703000-5711600	Weak transcription	Ovary	ovary
37	chr7:5703800-5710600	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr7:5704000-5707600	Enhancers	iPS-18 Cell Line	embryonic stem cell
39	chr7:5704000-5707800	Enhancers	HUES6 Cell Line	embryonic stem cell
40	chr7:5704200-5710000	Weak transcription	HepG2	liver
41	chr7:5705200-5707600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr7:5705200-5710200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr7:5705200-5710400	Weak transcription	HMEC	breast
44	chr7:5705200-5711600	Weak transcription	NHDF-Ad	bronchial
45	chr7:5705400-5707600	Weak transcription	Primary B cells from cord blood	blood
46	chr7:5705400-5708000	Weak transcription	Osteobl	bone
47	chr7:5705400-5708200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr7:5705400-5708200	Weak transcription	Fetal Brain Male	brain
49	chr7:5705400-5710200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr7:5705400-5710400	Weak transcription	Duodenum Smooth Muscle	Duodenum

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