Variant report

Variant	rs1416920
Chromosome Location	chr6:28302784-28302785
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:30)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:30 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:28109265..28112090-chr6:28302311..28305142,2	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	chr6:27796630..27800125-chr6:28302655..28305022,3	K562	blood:
6	chr6:28247415..28251168-chr6:28301808..28306623,8	K562	blood:
7	chr6:28293963..28296628-chr6:28301528..28305497,4	MCF-7	breast:
8	chr6:27774293..27778194-chr6:28301096..28304976,3	K562	blood:
9	chr6:28109273..28111011-chr6:28302779..28305242,3	MCF-7	breast:
10	chr6:28218301..28221476-chr6:28302207..28305180,4	MCF-7	breast:
11	chr6:28300850..28305636-chr6:28315212..28320749,12	MCF-7	breast:
12	chr6:28245880..28256877-chr6:28299741..28307557,21	K562	blood:
13	chr6:28234248..28238647-chr6:28302210..28305266,7	K562	blood:
14	chr6:28103055..28111556-chr6:28296771..28308203,17	K562	blood:
15	chr6:28233221..28238495-chr6:28301018..28307259,12	K562	blood:
16	chr6:27804731..27806517-chr6:28302178..28303810,2	MCF-7	breast:
17	chr6:28184981..28190782-chr6:28297491..28307222,23	K562	blood:
18	chr6:28182366..28191375-chr6:28300021..28306741,17	K562	blood:
19	chr6:28235909..28238714-chr6:28300665..28303049,3	MCF-7	breast:
20	chr6:28191609..28196785-chr6:28301378..28305522,8	K562	blood:
21	chr6:28302165..28304933-chr6:28366158..28368845,2	K562	blood:
22	chr6:28126892..28131515-chr6:28301205..28304944,6	K562	blood:
23	chr6:28232678..28234825-chr6:28301975..28304232,2	MCF-7	breast:
24	chr6:28285662..28290423-chr6:28300603..28305447,9	MCF-7	breast:
25	chr6:28218514..28221776-chr6:28301462..28305432,7	K562	blood:
26	chr6:28248171..28250694-chr6:28301952..28304469,4	MCF-7	breast:
27	chr6:27857690..27865363-chr6:28300493..28306970,14	K562	blood:
28	chr6:27802790..27806364-chr6:28301138..28304856,3	K562	blood:
29	chr6:28218514..28221956-chr6:28302143..28305192,6	K562	blood:
30	chr6:27857994..27864853-chr6:28300493..28305532,13	K562	blood:

No data

Variant related genes	Relation type
ENSG00000196747	Chromatin interaction
ENSG00000184348	Chromatin interaction
ENSG00000137185	Chromatin interaction
ENSG00000198315	Chromatin interaction
ENSG00000235109	Chromatin interaction
ENSG00000226314	Chromatin interaction
ENSG00000238610	Chromatin interaction
ENSG00000187626	Chromatin interaction
ENSG00000261839	Chromatin interaction
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction
ENSG00000158691	Chromatin interaction
ENSG00000137338	Chromatin interaction
ENSG00000217862	Chromatin interaction
ENSG00000197062	Chromatin interaction
ENSG00000233822	Chromatin interaction
ENSG00000176933	Chromatin interaction
ENSG00000189298	Chromatin interaction
ENSG00000203813	Chromatin interaction
ENSG00000270326	Chromatin interaction
ENSG00000196331	Chromatin interaction
ENSG00000197914	Chromatin interaction
ENSG00000269293	Chromatin interaction
ENSG00000185130	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 17 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1016070	0.86[CHB][hapmap]
rs1150711	0.81[TSI][hapmap]
rs12000	0.86[CHB][hapmap];0.80[GIH][hapmap];0.87[JPT][hapmap]
rs12180820	1.00[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16893947	0.80[CHD][hapmap]
rs16893970	0.80[CHD][hapmap]
rs1997660	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2021745	0.86[CHB][hapmap]
rs2108926	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]
rs2531813	0.86[CHB][hapmap]
rs2531814	0.86[CHB][hapmap]
rs2859372	0.86[CHB][hapmap]
rs2859373	0.86[CHB][hapmap]
rs2859374	0.86[CHB][hapmap]
rs4713158	0.86[EUR][1000 genomes]
rs6456815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6936644	0.92[ASN][1000 genomes]
rs6942030	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs707907	0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs758398	0.86[CHB][hapmap];0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7772827	1.00[CEU][hapmap];0.82[CHB][hapmap];0.91[CHD][hapmap];0.80[GIH][hapmap];0.86[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs853683	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs853690	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs853693	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs9468333	0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs9468334	0.89[ASN][1000 genomes]
rs9468344	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];0.98[MKK][hapmap];1.00[TSI][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]

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

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs1416920	AL022393.7	cis	Muscle Skeletal	GTEx
rs1416920	AL022393.7	cis	Heart Left Ventricle	GTEx
rs1416920	ZKSCAN3	cis	parietal	SCAN
rs1416920	ZNF323	cis	parietal	SCAN
rs1416920	ZNF187	cis	cerebellum	SCAN
rs1416920	AL022393.7	cis	Nerve Tibial	GTEx
rs1416920	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs1416920	AL022393.7	cis	Esophagus Muscularis	GTEx
rs1416920	ZKSCAN3	cis	cerebellum	SCAN
rs1416920	HIST1H2BN	cis	cerebellum	SCAN
rs1416920	ZSCAN23	cis	cerebellum	SCAN
rs1416920	ZSCAN23	cis	Artery Tibial	GTEx
rs1416920	ZSCAN31	cis	lung	GTEx
rs1416920	ZSCAN23	cis	parietal	SCAN
rs1416920	ZNF192	cis	cerebellum	SCAN
rs1416920	RP5-874C20.3	cis	Thyroid	GTEx
rs1416920	NKAPL	cis	parietal	SCAN

Chromatin state (count:88 , 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	chr6:28295400-28302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
3	chr6:28295400-28303000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr6:28295400-28303000	Weak transcription	Thymus	Thymus
5	chr6:28295600-28302800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr6:28295600-28302800	Weak transcription	Fetal Brain Male	brain
7	chr6:28295800-28302800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr6:28297000-28302800	Weak transcription	Colonic Mucosa	Colon
9	chr6:28297000-28303400	Weak transcription	Gastric	stomach
10	chr6:28297200-28302800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:28297200-28302800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr6:28297200-28302800	Weak transcription	Duodenum Mucosa	Duodenum
13	chr6:28297200-28302800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr6:28297200-28302800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr6:28297200-28303000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr6:28297400-28302800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr6:28297400-28302800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr6:28297400-28302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr6:28297400-28302800	Weak transcription	Fetal Intestine Large	intestine
20	chr6:28297400-28302800	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:28297400-28302800	Weak transcription	Psoas Muscle	Psoas
22	chr6:28297400-28303400	Weak transcription	Ovary	ovary
23	chr6:28297400-28303400	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr6:28297600-28302800	Weak transcription	Fetal Muscle Leg	muscle
25	chr6:28298000-28302800	Weak transcription	Liver	Liver
26	chr6:28298200-28302800	Weak transcription	Skeletal Muscle Male	skeletal muscle
27	chr6:28300800-28303000	Flanking Active TSS	K562	blood
28	chr6:28301000-28302800	Weak transcription	Aorta	Aorta
29	chr6:28301600-28302800	Weak transcription	Esophagus	oesophagus
30	chr6:28301600-28303400	Weak transcription	Lung	lung
31	chr6:28302200-28302800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr6:28302200-28302800	Enhancers	Brain Anterior Caudate	brain
33	chr6:28302200-28302800	Enhancers	Brain Hippocampus Middle	brain
34	chr6:28302200-28302800	Active TSS	Fetal Brain Female	brain
35	chr6:28302200-28302800	Enhancers	Pancreatic Islets	Pancreatic Islet
36	chr6:28302200-28302800	Enhancers	Dnd41	blood
37	chr6:28302200-28303000	Enhancers	Primary T helper naive cells from peripheral blood	blood
38	chr6:28302200-28303000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr6:28302200-28303000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
40	chr6:28302200-28303200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr6:28302200-28303200	Flanking Active TSS	Fetal Heart	heart
42	chr6:28302200-28305400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr6:28302400-28302800	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
44	chr6:28302400-28302800	Active TSS	Adipose Nuclei	Adipose
45	chr6:28302400-28302800	Enhancers	Brain Germinal Matrix	brain
46	chr6:28302400-28302800	Enhancers	Brain Substantia Nigra	brain
47	chr6:28302400-28302800	Flanking Active TSS	Fetal Kidney	kidney
48	chr6:28302400-28302800	Enhancers	Fetal Stomach	stomach
49	chr6:28302400-28302800	Enhancers	Left Ventricle	heart
50	chr6:28302400-28302800	Enhancers	Pancreas	Pancrea

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