Variant report

Variant	rs6518352
Chromosome Location	chr21:45646698-45646699
allele	A/G
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:45634893..45639040-chr21:45644730..45647153,3	K562	blood:
2	chr21:45646352..45648342-chr21:45670015..45672115,2	MCF-7	breast:
3	chr21:45634893..45639040-chr21:45644730..45647153,4	K562	blood:
4	chr21:45638620..45641640-chr21:45644035..45648127,5	MCF-7	breast:
5	chr21:45626756..45628836-chr21:45644780..45646727,2	MCF-7	breast:
6	chr21:45621066..45623314-chr21:45644215..45646761,3	MCF-7	breast:
7	chr21:45644990..45647896-chr21:45648106..45650288,2	K562	blood:
8	chr21:45625272..45628072-chr21:45645841..45648362,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000232010	Chromatin interaction
ENSG00000232124	Chromatin interaction
ENSG00000232698	Chromatin interaction
ENSG00000142182	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1048710	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11701174	0.81[EUR][1000 genomes]
rs12482807	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13052840	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2070554	0.90[TSI][hapmap]
rs2329712	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838530	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838531	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2838532	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2838533	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34549906	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3746963	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4143384	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4568033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818887	0.83[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818889	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4818892	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4819388	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.80[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7276227	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7278940	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.97[GIH][hapmap];0.94[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7283760	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8126734	0.87[ASN][1000 genomes]
rs8127002	0.88[ASN][1000 genomes]
rs8127114	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8128292	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv33817	chr21:45169412-46031810	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	121 gene(s)	inside rSNPs	diseases
2	nsv913887	chr21:45344799-45670770	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
3	nsv1064420	chr21:45460089-45814986	Enhancers Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
4	nsv544472	chr21:45460089-45814986	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	nsv432155	chr21:45479055-45772388	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	esv1825445	chr21:45535566-45754936	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	esv1817474	chr21:45540607-45773102	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription 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	65 gene(s)	inside rSNPs	diseases
8	nsv533679	chr21:45551026-45768578	Enhancers Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
9	nsv913898	chr21:45555079-45941566	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS 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	74 gene(s)	inside rSNPs	diseases
10	nsv428042	chr21:45560437-45848190	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
11	nsv913901	chr21:45615741-45665330	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
12	nsv913902	chr21:45615741-45709153	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
13	nsv470906	chr21:45627976-45661343	Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
14	nsv459295	chr21:45629565-45849864	Genic enhancers Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
15	nsv587740	chr21:45629565-45849864	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
16	nsv913903	chr21:45630608-45657970	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
17	nsv913904	chr21:45636881-45700641	Genic enhancers Enhancers Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv913905	chr21:45640629-45696025	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6518352	PSMG1	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:45628600-45659600	Weak transcription	Right Atrium	heart
2	chr21:45628800-45646800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr21:45632200-45659600	Weak transcription	Fetal Kidney	kidney
4	chr21:45638800-45649000	Weak transcription	Right Ventricle	heart
5	chr21:45639000-45648600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr21:45639200-45647400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr21:45639200-45647800	Weak transcription	Colonic Mucosa	Colon
8	chr21:45639600-45648200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr21:45639800-45659400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr21:45640000-45648400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:45640000-45648800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr21:45640000-45659000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr21:45640200-45648400	Weak transcription	HUES6 Cell Line	embryonic stem cell
14	chr21:45640600-45647600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr21:45640600-45653400	Weak transcription	Primary monocytes fromperipheralblood	blood
16	chr21:45641200-45648000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr21:45641200-45648200	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr21:45641600-45654400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr21:45643200-45648200	Weak transcription	Brain Anterior Caudate	brain
20	chr21:45643400-45647400	Weak transcription	Fetal Intestine Large	intestine
21	chr21:45643400-45653600	Weak transcription	HepG2	liver
22	chr21:45643400-45659600	Weak transcription	Hela-S3	cervix
23	chr21:45643600-45646800	Weak transcription	Lung	lung
24	chr21:45643600-45647400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr21:45643600-45647600	Weak transcription	Psoas Muscle	Psoas
26	chr21:45643600-45647800	Weak transcription	Primary B cells from cord blood	blood
27	chr21:45643600-45647800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr21:45643600-45648000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr21:45643600-45648000	Weak transcription	Brain Angular Gyrus	brain
30	chr21:45643600-45648000	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr21:45643600-45648200	Weak transcription	Adipose Nuclei	Adipose
32	chr21:45643600-45650000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr21:45643600-45652400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr21:45643600-45653400	Weak transcription	Left Ventricle	heart
35	chr21:45643600-45653400	Weak transcription	HMEC	breast
36	chr21:45643600-45653800	Weak transcription	Stomach Mucosa	stomach
37	chr21:45643600-45654400	Weak transcription	NHEK	skin
38	chr21:45643600-45654800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr21:45643800-45646800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
40	chr21:45643800-45646800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr21:45643800-45647600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr21:45644800-45659400	Weak transcription	Small Intestine	intestine
43	chr21:45645200-45648000	Weak transcription	Primary T cells from cord blood	blood
44	chr21:45645200-45659200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr21:45645400-45648400	Weak transcription	Stomach Smooth Muscle	stomach
46	chr21:45645400-45653200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr21:45645600-45651600	Strong transcription	Esophagus	oesophagus
48	chr21:45645800-45648000	Weak transcription	Pancreas	Pancrea
49	chr21:45645800-45651200	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr21:45645800-45651600	Strong transcription	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links