Variant report

Variant	rs12200953
Chromosome Location	chr6:117924602-117924603
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:27)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:27 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:117923017-117924659	MCF-7	breast:	n/a	n/a
2	HCFC1	chr6:117922825-117924670	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr6:117922828-117924695	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr6:117922642-117924733	GM19099	blood:	n/a	n/a
5	MXI1	chr6:117922506-117924908	IMR90	lung:	n/a	n/a
6	MXI1	chr6:117922355-117924706	SK-N-SH	brain:	n/a	n/a
7	TBP	chr6:117923474-117924644	GM12878	blood:	n/a	n/a
8	POLR2A	chr6:117923033-117924621	ProgFib	skin:	n/a	n/a
9	POLR2A	chr6:117922692-117924739	Raji	blood:	n/a	n/a
10	POLR2A	chr6:117922558-117924652	K562	blood:	n/a	n/a
11	MTA3	chr6:117922656-117924675	GM12878	blood:	n/a	n/a
12	POLR2A	chr6:117922530-117924637	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr6:117922376-117925418	GM12891	blood:	n/a	n/a
14	POLR2A	chr6:117922534-117924618	HepG2	liver:	n/a	n/a
15	POLR2A	chr6:117922675-117924713	GM12878	blood:	n/a	n/a
16	POLR2A	chr6:117920430-117924813	K562	blood:	n/a	n/a
17	MAX	chr6:117924545-117924779	GM12878	blood:	n/a	n/a
18	POLR2A	chr6:117922669-117924627	GM18526	blood:	n/a	n/a
19	POLR2A	chr6:117922537-117924792	GM12878	blood:	n/a	n/a
20	POLR2A	chr6:117922540-117924646	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr6:117923142-117924697	U87	brain:	n/a	n/a
22	MYBL2	chr6:117922971-117924626	HepG2	liver:	n/a	n/a
23	POLR2A	chr6:117923305-117924624	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr6:117922501-117924938	GM12878	blood:	n/a	n/a
25	TBL1XR1	chr6:117923077-117924620	K562	blood:	n/a	n/a
26	POLR2A	chr6:117922374-117924775	SK-N-MC	brain:	n/a	n/a
27	POLR2A	chr6:117922680-117924680	GM18505	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:117805729..117808252-chr6:117923714..117925422,2	K562	blood:
2	chr6:117901608..117904180-chr6:117924058..117926949,2	K562	blood:
3	chr6:117919537..117925760-chr6:117993513..117997816,10	K562	blood:
4	chr6:117798788..117807313-chr6:117921918..117925735,11	MCF-7	breast:
5	chr6:117803575..117805462-chr6:117921337..117926516,4	K562	blood:
6	chr6:117778227..117782608-chr6:117922454..117926248,4	MCF-7	breast:
7	chr6:117803211..117805462-chr6:117921337..117926538,8	K562	blood:
8	chr6:117919854..117927630-chr6:117992313..117999313,9	K562	blood:
9	chr6:117921339..117924676-chr6:117954310..117957194,3	MCF-7	breast:
10	chr6:117920370..117923452-chr6:117923960..117927734,3	MCF-7	breast:

No data

Variant related genes	Relation type
GOPC	TF binding region
ENSG00000207461	Chromatin interaction
ENSG00000153989	Chromatin interaction
ENSG00000218233	Chromatin interaction
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10456911	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10456912	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457319	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10457320	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10484301	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10872154	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];0.82[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153674	1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11153691	0.90[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs11754735	0.87[AFR][1000 genomes]
rs11758156	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11759685	0.82[EUR][1000 genomes]
rs12191882	0.82[EUR][1000 genomes]
rs12192117	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12192219	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12193035	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12194014	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196716	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12196946	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12197399	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12202157	0.82[AFR][1000 genomes]
rs12202612	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12205852	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12208894	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209222	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12209476	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12209927	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12210860	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12215701	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374604	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17637404	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17818735	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2134088	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs41291926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56020204	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72965600	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967214	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72967253	0.92[AFR][1000 genomes];0.86[EUR][1000 genomes]
rs916305	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs929059	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9320605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9481727	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9489220	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9688605	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9766117	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9766656	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs9766945	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];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9766959	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];0.85[ASN][1000 genomes]
rs9767675	1.00[CHB][hapmap];1.00[JPT][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	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12200953	TSPYL1	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117924000-117924800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
2	chr6:117924000-117924800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr6:117924000-117924800	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
4	chr6:117924000-117924800	Flanking Active TSS	Dnd41	blood
5	chr6:117924000-117924800	Flanking Active TSS	HMEC	breast
6	chr6:117924200-117924800	Flanking Active TSS	A549	lung
7	chr6:117924200-117924800	Flanking Active TSS	GM12878-XiMat	blood
8	chr6:117924200-117925000	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr6:117924200-117925200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr6:117924400-117924800	Enhancers	Primary T cells from cord blood	blood
11	chr6:117924400-117924800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr6:117924400-117924800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
13	chr6:117924400-117925800	Enhancers	Fetal Intestine Small	intestine
14	chr6:117924400-117926000	Enhancers	Fetal Intestine Large	intestine
15	chr6:117924600-117924800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr6:117924600-117924800	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr6:117924600-117924800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr6:117924600-117924800	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr6:117924600-117924800	Enhancers	Brain Angular Gyrus	brain
20	chr6:117924600-117924800	Enhancers	Brain Hippocampus Middle	brain
21	chr6:117924600-117924800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:117924600-117924800	Enhancers	Skeletal Muscle Male	skeletal muscle
23	chr6:117924600-117924800	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr6:117924600-117924800	Active TSS	NHEK	skin
25	chr6:117924600-117925000	Enhancers	Primary T killer memory cells from peripheral blood	blood
26	chr6:117924600-117925000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr6:117924600-117925200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:117924600-117925200	Enhancers	Liver	Liver
29	chr6:117924600-117925200	Enhancers	K562	blood
30	chr6:117924600-117926200	Weak transcription	Primary B cells from peripheral blood	blood
31	chr6:117924600-117926200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr6:117924600-117926200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr6:117924600-117926200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr6:117924600-117926200	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr6:117924600-117926200	Weak transcription	Stomach Mucosa	stomach
36	chr6:117924600-117926400	Weak transcription	Brain Cingulate Gyrus	brain
37	chr6:117924600-117928200	Weak transcription	Primary monocytes fromperipheralblood	blood
38	chr6:117924600-117928400	Weak transcription	Monocytes-CD14+_RO01746	blood
39	chr6:117924600-117933200	Weak transcription	HUES6 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links