Variant report

Variant	rs7745560
Chromosome Location	chr6:86288921-86288922
allele	A/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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:86287466..86289317-chr6:86353179..86355732,2	MCF-7	breast:
2	chr6:86286722..86289673-chr6:86387180..86389276,2	MCF-7	breast:
3	chr6:86287818..86291892-chr6:86385672..86390313,6	MCF-7	breast:
4	chr6:86281475..86283897-chr6:86288113..86290341,2	K562	blood:
5	chr6:86288405..86291520-chr6:86301409..86305260,4	K562	blood:
6	chr6:86286697..86290056-chr6:86301886..86305465,5	MCF-7	breast:
7	chr6:86287653..86290758-chr6:86386971..86389926,3	K562	blood:
8	chr6:86288404..86291892-chr6:86352318..86354794,4	MCF-7	breast:
9	chr6:86285488..86287926-chr6:86288888..86290773,2	MCF-7	breast:
10	chr6:86279748..86283159-chr6:86286791..86290808,4	K562	blood:
11	chr6:86288385..86291520-chr6:86301409..86305260,7	K562	blood:

No data

Variant related genes	Relation type
ENSG00000135317	Chromatin interaction
ENSG00000135316	Chromatin interaction
ENSG00000203875	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12055597	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs12524836	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs12528808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12664908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1570311	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs3812137	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap]
rs3812139	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4373339	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs4400191	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs4458647	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4487548	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs494688	0.85[JPT][hapmap]
rs6900270	1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap]
rs6902638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6902904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6906618	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap]
rs6910543	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap]
rs6913634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap]
rs6930543	0.85[AFR][1000 genomes]
rs6930790	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs6942065	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7744309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7749600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs7752105	0.83[AFR][1000 genomes]
rs7753022	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs7760309	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs7766284	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs7771187	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7771366	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9344530	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9344538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9353319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9353321	0.80[AFR][1000 genomes]
rs9353324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs9359655	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9359656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9362223	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9444356	0.80[AFR][1000 genomes]
rs9450278	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450286	1.00[ASW][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap]
rs9450294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs9450295	0.81[AFR][1000 genomes]
rs9450299	0.85[AFR][1000 genomes]
rs9450300	0.83[AFR][1000 genomes]
rs9450307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs9450308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap]
rs9450313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][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	nsv1022445	chr6:85972678-86392968	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
2	nsv538349	chr6:85972678-86392968	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	esv3326486	chr6:86020165-86292456	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
4	nsv886333	chr6:86199243-86289415	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv886334	chr6:86214507-86394403	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	124 gene(s)	inside rSNPs	diseases
6	esv1792638	chr6:86224053-86336300	Weak transcription Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
7	esv3351743	chr6:86286282-86308720	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7745560	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs7745560	NT5E	cis	lymphoblastoid	seeQTL
rs7745560	C6orf160	cis	multi-tissue	Pritchard

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86208800-86289200	Weak transcription	Pancreas	Pancrea
2	chr6:86222600-86289400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
4	chr6:86233800-86289200	Weak transcription	Spleen	Spleen
5	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
6	chr6:86244200-86289200	Weak transcription	Gastric	stomach
7	chr6:86252800-86289600	Weak transcription	Esophagus	oesophagus
8	chr6:86263000-86289400	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr6:86263000-86289600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr6:86265600-86289800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr6:86266400-86290000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr6:86272000-86290200	Weak transcription	Fetal Muscle Leg	muscle
13	chr6:86277600-86289200	Weak transcription	Lung	lung
14	chr6:86278200-86302600	Weak transcription	Ovary	ovary
15	chr6:86278400-86291400	Weak transcription	Adipose Nuclei	Adipose
16	chr6:86279200-86289200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr6:86280200-86290200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr6:86281200-86289600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:86281400-86289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
22	chr6:86281600-86290000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr6:86281600-86290000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:86281600-86290200	Weak transcription	GM12878-XiMat	blood
25	chr6:86281600-86291800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:86281800-86290400	Weak transcription	Fetal Muscle Trunk	muscle
27	chr6:86282000-86289200	Weak transcription	Fetal Intestine Large	intestine
28	chr6:86282200-86290400	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr6:86282200-86291600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:86282400-86290200	Weak transcription	Placenta	Placenta
31	chr6:86283000-86290200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr6:86283400-86289000	Weak transcription	Primary T helper cells fromperipheralblood	blood
33	chr6:86283600-86290200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr6:86284400-86292000	Enhancers	Stomach Mucosa	stomach
35	chr6:86285000-86290400	Weak transcription	Small Intestine	intestine
36	chr6:86285200-86289200	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr6:86285200-86290200	Weak transcription	Aorta	Aorta
38	chr6:86285400-86290400	Weak transcription	Hela-S3	cervix
39	chr6:86285600-86289200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr6:86285600-86289600	Weak transcription	NH-A	brain
41	chr6:86285600-86290000	Weak transcription	Duodenum Mucosa	Duodenum
42	chr6:86285600-86290200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr6:86285600-86290200	Weak transcription	HSMM	muscle
44	chr6:86285600-86290600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr6:86285600-86290800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr6:86285800-86289600	Weak transcription	HMEC	breast
47	chr6:86286000-86291200	Enhancers	Skeletal Muscle Female	skeletal muscle
48	chr6:86286200-86289600	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr6:86286400-86289000	Weak transcription	A549	lung
50	chr6:86286400-86289400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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