Variant report

Variant	rs7771366
Chromosome Location	chr6:86291911-86291912
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SETDB1	chr6:86290959-86292073	U2OS	brain:	n/a	n/a
2	CBX3	chr6:86290464-86292040	K562	blood:	n/a	n/a
3	KAP1	chr6:86290879-86292099	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:86289336..86292710-chr6:86302948..86306481,4	MCF-7	breast:

Variant related genes	Relation type
SNX14	TF binding region
ENSG00000135317	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs12055597	1.00[CHB][hapmap];1.00[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];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662033	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12664908	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1570311	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs1590279	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2229524	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3812137	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];0.87[ASN][1000 genomes]
rs3812139	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs4144167	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4327657	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4373339	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs4400191	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap]
rs4458647	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4487548	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs4565270	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs494688	0.85[JPT][hapmap]
rs59744370	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6900270	1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6902638	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6902904	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
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];1.00[CHD][hapmap];1.00[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];0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6913634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6923017	0.85[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6930543	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6930790	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[ASN][1000 genomes]
rs6942065	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs73751215	0.87[ASN][1000 genomes]
rs7744309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7745560	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]
rs7749600	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7752105	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7753022	1.00[CHB][hapmap];1.00[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];0.87[ASN][1000 genomes]
rs7775016	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap]
rs7775788	0.88[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9344528	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs9344530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs9344538	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9351063	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9351066	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9353319	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[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];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9353321	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9353323	0.90[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9353324	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9359655	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs9359656	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9362223	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9362224	0.81[ASN][1000 genomes]
rs9362225	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9362226	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444353	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9444356	0.95[AFR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9450278	1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap]
rs9450280	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9450286	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MKK][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs9450289	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450295	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450299	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9450300	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450304	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450307	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450309	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9450313	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
5	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
6	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
rs7771366	NT5E	cis	lymphoblastoid	seeQTL
rs7771366	NT5E	Cis_1M	lymphoblastoid	RTeQTL
rs7771366	NT5E	cis	Thyroid	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:86224200-86302600	Weak transcription	Colonic Mucosa	Colon
2	chr6:86243400-86301400	Weak transcription	Thymus	Thymus
3	chr6:86278200-86302600	Weak transcription	Ovary	ovary
4	chr6:86280000-86301400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr6:86281400-86301600	Weak transcription	Fetal Thymus	thymus
6	chr6:86284400-86292000	Enhancers	Stomach Mucosa	stomach
7	chr6:86286600-86302000	Weak transcription	Rectal Smooth Muscle	rectum
8	chr6:86286800-86297600	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:86288200-86292600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr6:86288200-86301400	Weak transcription	Fetal Heart	heart
11	chr6:86288400-86292800	Weak transcription	Brain Cingulate Gyrus	brain
12	chr6:86288400-86295600	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr6:86288600-86295400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:86289200-86301000	Weak transcription	Rectal Mucosa Donor 29	rectum
15	chr6:86289400-86292800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
16	chr6:86289800-86297600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr6:86290000-86300800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr6:86290000-86301000	Weak transcription	Brain Hippocampus Middle	brain
19	chr6:86290200-86301800	Weak transcription	Stomach Smooth Muscle	stomach
20	chr6:86290400-86301400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr6:86290400-86302400	Weak transcription	Placenta	Placenta
22	chr6:86290800-86295600	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr6:86290800-86296400	Weak transcription	Fetal Stomach	stomach
24	chr6:86290800-86301400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr6:86290800-86302000	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:86291000-86292000	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
27	chr6:86291000-86292000	Enhancers	HepG2	liver
28	chr6:86291000-86294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:86291000-86295400	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr6:86291000-86295600	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr6:86291000-86296400	Weak transcription	Left Ventricle	heart
32	chr6:86291000-86296400	Weak transcription	Psoas Muscle	Psoas
33	chr6:86291000-86297000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr6:86291000-86297200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr6:86291000-86297200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr6:86291000-86302000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
37	chr6:86291000-86302000	Weak transcription	HSMM	muscle
38	chr6:86291000-86302600	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr6:86291200-86298600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr6:86291200-86300600	Weak transcription	Skeletal Muscle Female	skeletal muscle
41	chr6:86291200-86301000	Weak transcription	Primary T cells from cord blood	blood
42	chr6:86291200-86301200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr6:86291200-86301200	Weak transcription	Hela-S3	cervix
44	chr6:86291200-86301200	Weak transcription	NHEK	skin
45	chr6:86291200-86301400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr6:86291200-86301800	Weak transcription	HUVEC	blood vessel
47	chr6:86291200-86302600	Weak transcription	Pancreas	Pancrea
48	chr6:86291200-86302600	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr6:86291200-86302800	Weak transcription	Gastric	stomach
50	chr6:86291400-86292000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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