Variant report

Variant	rs17684878
Chromosome Location	chr6:56702976-56702977
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:56702761..56706423-chr6:56707121..56709805,6	MCF-7	breast:
2	chr6:56672534..56675270-chr6:56701111..56703419,2	MCF-7	breast:
3	chr6:56701741..56705807-chr6:56706748..56710604,7	MCF-7	breast:
4	chr6:56702437..56704205-chr6:56705017..56706715,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000151914	Chromatin interaction
ENSG00000231441	Chromatin interaction

Extended variants
information (count: 135 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10498812	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs10498813	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11756551	0.85[EUR][1000 genomes]
rs11968575	0.81[CEU][hapmap];0.81[MEX][hapmap]
rs11970648	1.00[CEU][hapmap];0.81[MEX][hapmap]
rs13190784	1.00[MEX][hapmap];0.81[TSI][hapmap]
rs13190854	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13192540	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13192931	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13194625	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13194904	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs13195601	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13198204	0.89[EUR][1000 genomes]
rs13198597	0.94[CEU][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13200166	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];0.83[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs13200559	0.84[EUR][1000 genomes]
rs13200768	0.88[EUR][1000 genomes]
rs13200868	0.82[EUR][1000 genomes]
rs13201639	0.89[EUR][1000 genomes]
rs13201733	0.89[EUR][1000 genomes]
rs13203000	0.81[CEU][hapmap]
rs13203148	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13203327	0.85[EUR][1000 genomes]
rs13203681	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13204466	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13205667	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs13207768	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13208409	0.81[EUR][1000 genomes]
rs13211879	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13214893	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13215883	0.94[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13217390	0.81[CEU][hapmap]
rs13218913	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs13220618	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13220628	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs13220851	0.91[EUR][1000 genomes]
rs1610156	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1610157	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16888171	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs16888184	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16888186	0.87[CEU][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16888189	0.81[TSI][hapmap]
rs17684730	0.89[EUR][1000 genomes]
rs17684748	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17684772	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17684784	1.00[CEU][hapmap];1.00[GIH][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs17684802	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs17684884	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17684941	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17751966	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17751977	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17752002	0.89[EUR][1000 genomes]
rs17752046	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs17752106	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17752213	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1903332	0.94[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28360570	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3002010	0.81[CEU][hapmap]
rs3002011	0.80[CEU][hapmap]
rs34083827	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs34171958	0.90[EUR][1000 genomes]
rs34228698	0.89[EUR][1000 genomes]
rs34359353	0.90[EUR][1000 genomes]
rs34425815	0.88[EUR][1000 genomes]
rs34500949	0.84[EUR][1000 genomes]
rs34520435	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs34612783	0.88[EUR][1000 genomes]
rs34614087	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34640766	0.89[EUR][1000 genomes]
rs34866877	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34896026	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34966024	0.83[EUR][1000 genomes]
rs35073881	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35080938	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35081015	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35225175	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35242294	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35251663	0.88[EUR][1000 genomes]
rs35407078	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35439100	0.97[EUR][1000 genomes]
rs35440408	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs35440822	0.90[EUR][1000 genomes]
rs35461301	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35566812	0.87[EUR][1000 genomes]
rs35609883	0.89[EUR][1000 genomes]
rs35642890	0.89[EUR][1000 genomes]
rs35696739	0.89[EUR][1000 genomes]
rs35828379	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs35851452	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35873865	0.87[EUR][1000 genomes]
rs35886823	0.89[EUR][1000 genomes]
rs35986172	0.81[EUR][1000 genomes]
rs36022925	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36037734	0.89[EUR][1000 genomes]
rs36094082	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4299824	1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.85[MKK][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs4348308	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4371846	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4415160	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4457154	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs4532444	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4587171	0.83[CEU][hapmap];0.87[TSI][hapmap];0.86[EUR][1000 genomes]
rs56037312	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56368885	0.82[EUR][1000 genomes]
rs58980183	0.82[EUR][1000 genomes]
rs59432342	0.89[EUR][1000 genomes]
rs61601344	0.89[EUR][1000 genomes]
rs62411366	0.82[EUR][1000 genomes]
rs62411367	0.84[EUR][1000 genomes]
rs62411372	0.88[EUR][1000 genomes]
rs62411375	0.88[EUR][1000 genomes]
rs62411376	0.89[EUR][1000 genomes]
rs6904535	0.84[EUR][1000 genomes]
rs6905603	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6910414	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6914293	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6918949	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6928104	0.82[EUR][1000 genomes]
rs6934714	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71564854	0.89[EUR][1000 genomes]
rs71564855	0.90[EUR][1000 genomes]
rs71564856	0.89[EUR][1000 genomes]
rs71564861	0.89[EUR][1000 genomes]
rs71564863	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7758867	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7761501	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.89[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7761729	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7766565	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7771085	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7775182	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491933	chr6:56177722-57171010	Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv934026	chr6:56382056-57184218	Flanking Bivalent TSS/Enh Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	nsv533050	chr6:56504480-57297586	Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
4	nsv1021651	chr6:56569444-56966319	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv538228	chr6:56569444-56966319	Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17684878	DST	cis	cerebellum	SCAN
rs17684878	BMP5	cis	cerebellum	SCAN
rs17684878	BEND6	cis	parietal	SCAN

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:56674200-56703000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:56684000-56703800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr6:56684200-56705200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr6:56693000-56703800	Weak transcription	Psoas Muscle	Psoas
5	chr6:56693600-56705600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:56693800-56705400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr6:56694000-56705400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr6:56694200-56704800	Weak transcription	NH-A	brain
9	chr6:56697400-56704000	Weak transcription	Osteobl	bone
10	chr6:56698600-56703000	Weak transcription	Adipose Nuclei	Adipose
11	chr6:56699000-56703800	Weak transcription	Rectal Smooth Muscle	rectum
12	chr6:56699600-56705600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr6:56699800-56705200	Weak transcription	Right Ventricle	heart
14	chr6:56700400-56705800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr6:56701800-56704000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr6:56701800-56705400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr6:56701800-56705400	Enhancers	Fetal Heart	heart
18	chr6:56702000-56704200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr6:56702000-56704800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr6:56702000-56705800	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr6:56702200-56703000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr6:56702200-56703000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
23	chr6:56702200-56703000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
24	chr6:56702200-56703200	Enhancers	H1 Cell Line	embryonic stem cell
25	chr6:56702200-56703200	Enhancers	H9 Cell Line	embryonic stem cell
26	chr6:56702200-56703400	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
27	chr6:56702200-56703800	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr6:56702200-56703800	Enhancers	Skeletal Muscle Male	skeletal muscle
29	chr6:56702200-56703800	Enhancers	Skeletal Muscle Female	skeletal muscle
30	chr6:56702200-56704000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr6:56702200-56704000	Enhancers	A549	lung
32	chr6:56702200-56704400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr6:56702200-56705000	Enhancers	Brain Substantia Nigra	brain
34	chr6:56702200-56705200	Enhancers	Brain Anterior Caudate	brain
35	chr6:56702200-56705400	Enhancers	ES-I3 Cell Line	embryonic stem cell
36	chr6:56702200-56705800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr6:56702400-56703000	Genic enhancers	Muscle Satellite Cultured Cells	--
38	chr6:56702400-56703000	Enhancers	Placenta Amnion	Placenta Amnion
39	chr6:56702400-56703200	Enhancers	Brain Angular Gyrus	brain
40	chr6:56702400-56703200	Flanking Active TSS	Brain Hippocampus Middle	brain
41	chr6:56702400-56703600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr6:56702400-56703800	Enhancers	HSMMtube	muscle
43	chr6:56702400-56704000	Enhancers	Brain Cingulate Gyrus	brain
44	chr6:56702400-56704000	Weak transcription	Brain Germinal Matrix	brain
45	chr6:56702400-56704000	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr6:56702400-56704000	Weak transcription	Right Atrium	heart
47	chr6:56702400-56705400	Weak transcription	Fetal Muscle Leg	muscle
48	chr6:56702400-56705600	Weak transcription	Left Ventricle	heart
49	chr6:56702600-56703200	Enhancers	Colon Smooth Muscle	Colon
50	chr6:56702600-56703600	Enhancers	NHLF	lung

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