Variant report

Variant	rs882367
Chromosome Location	chr17:59494574-59494575
allele	A/C/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:69)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

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

No.	Distal block	Cell Line	Cell type
1	chr17:59494357..59495148-chr17:59658506..59659905,4	MCF-7	breast:
2	chr17:59493147..59495448-chr17:59892097..59894543,2	MCF-7	breast:
3	chr17:59492663..59495167-chr9:114775467..114777487,2	MCF-7	breast:
4	chr1:146966452..146967044-chr17:59494207..59494892,2	MCF-7	breast:
5	chr17:59494352..59494952-chr17:59914324..59915251,3	K562	blood:
6	chr17:59493559..59494860-chr17:59913361..59915150,9	MCF-7	breast:
7	chr17:59493566..59494700-chr17:59656941..59657984,3	MCF-7	breast:
8	chr14:67249480..67250181-chr17:59494053..59494794,2	MCF-7	breast:
9	chr17:59415713..59496229-chr20:49401322..49431802,760	MCF-7	breast:
10	chr17:59493872..59494826-chr17:59652030..59652868,2	MCF-7	breast:
11	chr17:59494089..59494792-chr20:52486104..52486943,2	MCF-7	breast:
12	chr17:59493870..59495355-chr17:59659930..59661309,18	MCF-7	breast:
13	chr17:59494016..59494906-chr17:59763936..59765128,4	MCF-7	breast:
14	chr17:59493988..59494767-chr3:24306189..24306755,2	MCF-7	breast:
15	chr17:59493417..59496032-chr17:59625729..59629317,97	MCF-7	breast:
16	chr17:59493892..59494828-chr17:59576917..59577790,2	MCF-7	breast:
17	chr17:59492572..59494838-chr19:47729176..47730869,2	MCF-7	breast:
18	chr17:59494281..59494852-chr17:59503602..59504167,2	MCF-7	breast:
19	chr17:59494019..59494763-chr17:59764356..59764946,3	MCF-7	breast:
20	chr17:59493836..59494762-chr17:59503116..59503965,2	MCF-7	breast:
21	chr17:59494290..59494793-chr6:95879433..95879983,2	MCF-7	breast:
22	chr17:59494306..59494857-chr17:59567859..59568771,2	MCF-7	breast:
23	chr17:59493991..59494795-chr17:59624310..59625594,4	MCF-7	breast:
24	chr17:59494095..59496860-chr20:45948764..45950975,2	MCF-7	breast:
25	chr17:59493926..59494895-chr17:59628082..59629124,4	K562	blood:
26	chr17:59470571..59471324-chr17:59494235..59494804,2	MCF-7	breast:
27	chr17:59492727..59496859-chr17:59625979..59629778,204	MCF-7	breast:
28	chr17:59494354..59494878-chr17:59541679..59542516,2	MCF-7	breast:
29	chr17:59494225..59494858-chr7:87587735..87588447,2	MCF-7	breast:
30	chr17:59493936..59494881-chr17:59660574..59661086,2	K562	blood:
31	chr17:59488616..59494924-chr20:52554630..52559372,9	MCF-7	breast:
32	chr15:51673157..51673657-chr17:59494266..59494829,2	MCF-7	breast:
33	chr17:59493625..59494921-chr20:52556210..52557219,4	MCF-7	breast:
34	chr17:59493881..59494826-chr17:59524236..59524948,2	MCF-7	breast:
35	chr17:59494041..59495579-chr3:64313876..64315822,2	MCF-7	breast:
36	chr17:59494263..59494887-chr17:59577122..59578055,2	MCF-7	breast:
37	chr17:59494215..59494948-chr17:59649107..59649849,2	MCF-7	breast:
38	chr17:59492520..59494967-chr20:48598399..48600896,2	MCF-7	breast:
39	chr17:59493298..59494870-chr17:59631334..59633396,6	MCF-7	breast:
40	chr17:59494056..59494800-chr20:52273275..52273785,2	MCF-7	breast:
41	chr17:59493984..59494640-chr17:59713138..59713801,2	MCF-7	breast:
42	chr17:59493495..59495755-chr17:59720945..59723473,2	MCF-7	breast:
43	chr17:59493437..59495595-chr17:59651010..59653757,53	MCF-7	breast:
44	chr17:59493965..59494883-chr17:76246708..76247257,2	MCF-7	breast:
45	chr17:59494210..59494854-chr17:59534651..59535156,2	MCF-7	breast:
46	chr17:59493881..59494594-chr20:49410988..49412155,5	MCF-7	breast:
47	chr17:59493919..59495381-chr17:59914241..59915409,17	MCF-7	breast:
48	chr17:59494105..59494914-chr20:49407137..49407911,2	MCF-7	breast:
49	chr17:59494113..59494948-chr17:59540643..59541507,2	MCF-7	breast:
50	chr17:59494436..59494956-chr17:59915499..59916446,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124216	Chromatin interaction
ENSG00000105327	Chromatin interaction
ENSG00000236352	Chromatin interaction
ENSG00000132475	Chromatin interaction
ENSG00000265134	Chromatin interaction
ENSG00000267137	Chromatin interaction
ENSG00000121075	Chromatin interaction
ENSG00000124243	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1076392	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2079795	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109019	0.83[CHD][hapmap];0.84[GIH][hapmap]
rs7214743	0.95[CEU][hapmap];0.96[EUR][1000 genomes]
rs740755	0.82[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs757608	1.00[CEU][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs758598	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs758599	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8064243	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs887258	0.82[JPT][hapmap]
rs9892365	1.00[CEU][hapmap];0.82[JPT][hapmap];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9905385	1.00[CEU][hapmap];0.85[CHD][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9907379	0.88[CHD][hapmap];0.85[GIH][hapmap]

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	nsv1065939	chr17:59283350-59517730	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	331 gene(s)	inside rSNPs	diseases
2	nsv833505	chr17:59323466-59518007	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	326 gene(s)	inside rSNPs	diseases
3	nsv833506	chr17:59362377-59562984	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	334 gene(s)	inside rSNPs	diseases
4	esv1796927	chr17:59460119-59495319	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	270 gene(s)	inside rSNPs	diseases
5	nsv908663	chr17:59464069-59521310	Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	278 gene(s)	inside rSNPs	diseases
6	nsv908665	chr17:59470193-59494574	Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Weak transcription Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	264 gene(s)	inside rSNPs	diseases
7	nsv908668	chr17:59471151-59494574	Weak transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	263 gene(s)	inside rSNPs	diseases
8	nsv908670	chr17:59471372-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	262 gene(s)	inside rSNPs	diseases
9	nsv908671	chr17:59475888-59494574	Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
10	nsv908672	chr17:59476062-59494574	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	255 gene(s)	inside rSNPs	diseases
11	nsv519931	chr17:59491281-59514461	Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	59 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs882367	NACA2	cis	cerebellum	SCAN
rs882367	TBX4	cis	cerebellum	SCAN
rs882367	MRC2	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:59491000-59494600	Enhancers	Lung	lung
2	chr17:59491000-59495600	Enhancers	Placenta	Placenta
3	chr17:59491000-59504200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:59491800-59494600	Enhancers	NHLF	lung
5	chr17:59493200-59494800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr17:59493400-59494600	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr17:59493400-59494800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr17:59493600-59494600	Enhancers	Spleen	Spleen
9	chr17:59493600-59494800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr17:59493600-59495400	Enhancers	A549	lung
11	chr17:59493800-59494600	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr17:59493800-59494600	Bivalent Enhancer	Primary neutrophils fromperipheralblood	blood
13	chr17:59493800-59494600	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr17:59493800-59494600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
15	chr17:59493800-59494600	Enhancers	Gastric	stomach
16	chr17:59493800-59494600	Enhancers	Right Atrium	heart
17	chr17:59493800-59494600	Flanking Active TSS	Osteobl	bone
18	chr17:59493800-59494800	Enhancers	Liver	Liver
19	chr17:59493800-59494800	Enhancers	Brain Angular Gyrus	brain
20	chr17:59493800-59494800	Enhancers	Fetal Heart	heart
21	chr17:59494000-59494600	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr17:59494000-59494600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr17:59494000-59494600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr17:59494000-59494600	Bivalent Enhancer	Primary B cells from cord blood	blood
25	chr17:59494000-59494600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
26	chr17:59494000-59494600	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
27	chr17:59494000-59494600	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
28	chr17:59494000-59494600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr17:59494000-59494600	Active TSS	Muscle Satellite Cultured Cells	--
30	chr17:59494000-59494600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
31	chr17:59494000-59494600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr17:59494000-59494600	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr17:59494000-59494600	Flanking Active TSS	Brain Substantia Nigra	brain
34	chr17:59494000-59494600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
35	chr17:59494000-59494600	Active TSS	Fetal Brain Female	brain
36	chr17:59494000-59494600	Active TSS	Fetal Kidney	kidney
37	chr17:59494000-59494600	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
38	chr17:59494000-59494600	Flanking Active TSS	Ovary	ovary
39	chr17:59494000-59494600	Active TSS	HSMM	muscle
40	chr17:59494000-59494800	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
41	chr17:59494000-59494800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr17:59494000-59494800	Bivalent Enhancer	Primary B cells from peripheral blood	blood
43	chr17:59494000-59494800	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
44	chr17:59494000-59494800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr17:59494000-59494800	Enhancers	Esophagus	oesophagus
46	chr17:59494000-59494800	Bivalent Enhancer	Fetal Brain Male	brain
47	chr17:59494000-59494800	Bivalent Enhancer	Fetal Intestine Small	intestine
48	chr17:59494000-59494800	Enhancers	Pancreas	Pancrea
49	chr17:59494000-59494800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
50	chr17:59494000-59494800	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach

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