Variant report

Variant	rs16893975
Chromosome Location	chr6:28302278-28302279
allele	C/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:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28230115..28232269-chr6:28300762..28302458,2	MCF-7	breast:
2	chr6:27775597..27780846-chr6:28300467..28304976,7	K562	blood:
3	chr6:28191649..28195458-chr6:28301378..28307708,9	K562	blood:
4	chr6:28099723..28110178-chr6:28301599..28306918,14	K562	blood:
5	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
6	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
7	chr11:62609140..62609640-chr6:28301755..28302653,2	NB4	blood:
8	chr6:27774293..27778194-chr6:28301096..28304976,3	K562	blood:
9	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
10	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
11	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
12	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
13	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
14	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
15	chr6:27804731..27806517-chr6:28302178..28303810,2	MCF-7	breast:
16	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
17	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
18	chr6:28235909..28238714-chr6:28300665..28303049,3	MCF-7	breast:
19	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
20	chr6:28302165..28304933-chr6:28366158..28368845,2	K562	blood:
21	chr6:28126892..28131515-chr6:28301205..28304944,6	K562	blood:
22	chr6:28232678..28234825-chr6:28301975..28304232,2	MCF-7	breast:
23	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:
24	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
25	chr6:28248171..28250694-chr6:28301952..28304469,4	MCF-7	breast:
26	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
27	chr6:27802790..27806364-chr6:28301138..28304856,3	K562	blood:
28	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
29	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000235109	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000270326	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000196747	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000185130	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000197062	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10484542	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1233710	0.85[CEU][hapmap];0.80[MEX][hapmap]
rs1416919	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1635	0.85[CEU][hapmap]
rs16893917	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893929	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16893973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2077474	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs213233	1.00[CHB][hapmap];0.97[CHD][hapmap]
rs2159275	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2281040	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2281041	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2299030	0.85[CEU][hapmap]
rs3800324	0.80[ASW][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.88[MKK][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3800327	1.00[CEU][hapmap]
rs4711167	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4713159	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs58019071	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59598126	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60568488	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60698636	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs723475	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];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs723476	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];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742535	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742536	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742539	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73742541	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73742544	0.83[AFR][1000 genomes]
rs73742545	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs742107	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs758397	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7750106	0.85[CEU][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830620	chr6:28173997-28348033	Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	51 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:28294800-28302800	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr6:28295400-28302400	Weak transcription	Brain Angular Gyrus	brain
3	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
4	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
6	chr6:28295600-28302400	Weak transcription	Brain Substantia Nigra	brain
7	chr6:28295600-28302600	Weak transcription	Stomach Mucosa	stomach
8	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
10	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr6:28297000-28302800	Weak transcription	Colonic Mucosa	Colon
12	chr6:28297000-28303400	Weak transcription	Gastric	stomach
13	chr6:28297200-28302400	Weak transcription	Adipose Nuclei	Adipose
14	chr6:28297200-28302400	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:28297200-28302400	Weak transcription	Pancreas	Pancrea
16	chr6:28297200-28302400	Weak transcription	Right Ventricle	heart
17	chr6:28297200-28302600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr6:28297200-28302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
19	chr6:28297200-28302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr6:28297200-28302800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr6:28297200-28302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr6:28297200-28302800	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr6:28297200-28303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr6:28297400-28302400	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr6:28297400-28302400	Weak transcription	HUES64 Cell Line	embryonic stem cell
26	chr6:28297400-28302400	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr6:28297400-28302400	Weak transcription	Fetal Stomach	stomach
28	chr6:28297400-28302400	Weak transcription	Left Ventricle	heart
29	chr6:28297400-28302400	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr6:28297400-28302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:28297400-28302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:28297400-28302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr6:28297400-28302800	Weak transcription	Fetal Intestine Large	intestine
34	chr6:28297400-28302800	Weak transcription	Fetal Muscle Trunk	muscle
35	chr6:28297400-28302800	Weak transcription	Psoas Muscle	Psoas
36	chr6:28297400-28303400	Weak transcription	Ovary	ovary
37	chr6:28297400-28303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr6:28297600-28302400	Weak transcription	Stomach Smooth Muscle	stomach
39	chr6:28297600-28302800	Weak transcription	Fetal Muscle Leg	muscle
40	chr6:28298000-28302800	Weak transcription	Liver	Liver
41	chr6:28298200-28302400	Weak transcription	Fetal Lung	lung
42	chr6:28298200-28302800	Weak transcription	Skeletal Muscle Male	skeletal muscle
43	chr6:28300400-28302400	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr6:28300800-28303000	Flanking Active TSS	K562	blood
45	chr6:28301000-28302800	Weak transcription	Aorta	Aorta
46	chr6:28301200-28302400	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr6:28301400-28302400	Enhancers	Rectal Smooth Muscle	rectum
48	chr6:28301600-28302800	Weak transcription	Esophagus	oesophagus
49	chr6:28301600-28303400	Weak transcription	Lung	lung
50	chr6:28301800-28302400	Weak transcription	Brain Germinal Matrix	brain

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