Variant report

Variant	rs1217411
Chromosome Location	chr1:114356125-114356126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GABPA	chr1:114353816-114356357	MCF-7	breast:	n/a	n/a
2	POLR2A	chr1:114355874-114356302	HL-60	blood:	n/a	n/a
3	EGR1	chr1:114353034-114356186	MCF-7	breast:	n/a	n/a
4	ZMIZ1	chr1:114355857-114356188	K562	blood:	n/a	n/a
5	POLR2A	chr1:114355916-114356219	MCF-7	breast:	n/a	n/a
6	ELF1	chr1:114353837-114356350	MCF-7	breast:	n/a	n/a
7	POLR2A	chr1:114355954-114356226	ECC-1	luminal epithelium:	n/a	n/a
8	POLR2A	chr1:114353991-114356331	SK-N-MC	brain:	n/a	n/a
9	SIN3AK20	chr1:114353597-114356350	MCF-7	breast:	n/a	n/a
10	HEY1	chr1:114355899-114356292	K562	blood:	n/a	n/a
11	POLR2A	chr1:114354373-114356136	U87	brain:	n/a	n/a
12	POLR2A	chr1:114355786-114356259	K562	blood:	n/a	n/a
13	GATA3	chr1:114355929-114356179	MCF-7	breast:	n/a	n/a
14	MYC	chr1:114356069-114356150	MCF-7	breast:	n/a	n/a
15	POLR2A	chr1:114355962-114356169	MCF-7	breast:	n/a	n/a
16	PML	chr1:114353843-114356314	MCF-7	breast:	n/a	n/a
17	JUN	chr1:114352049-114356471	K562	blood:	n/a	n/a
18	POLR2A	chr1:114354619-114356285	GM12891	blood:	n/a	n/a
19	POLR2A	chr1:114354069-114356279	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr1:114355832-114356158	ProgFib	skin:	n/a	n/a
21	EP300	chr1:114355983-114356173	K562	blood:	n/a	n/a
22	POLR2A	chr1:114354070-114356136	K562	blood:	n/a	n/a

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:114353911..114356847-chr1:114364689..114367754,3	K562	blood:
2	chr1:114351760..114356326-chr1:114471041..114474785,9	K562	blood:
3	chr1:114353393..114356662-chr20:49346921..49350434,3	MCF-7	breast:
4	chr1:113497285..113498867-chr1:114354926..114357337,2	K562	blood:
5	chr1:114354399..114356647-chr1:115051838..115054168,3	MCF-7	breast:
6	chr1:114352306..114358140-chr1:114445806..114450844,18	MCF-7	breast:
7	chr1:114353620..114357151-chr1:114445438..114449458,6	K562	blood:
8	chr1:114355402..114357827-chr1:114471686..114473610,2	K562	blood:
9	chr1:114354097..114356743-chr1:115299184..115300784,2	MCF-7	breast:
10	chr1:114355388..114357154-chr1:114463628..114466321,2	MCF-7	breast:
11	chr1:114308167..114310817-chr1:114354142..114357057,3	K562	blood:
12	chr1:114353683..114357770-chr1:114446246..114449576,8	K562	blood:
13	chr1:114353086..114356383-chr1:114467552..114475359,15	MCF-7	breast:
14	chr1:114353164..114356409-chr1:114439569..114442509,4	MCF-7	breast:
15	chr1:114352137..114357235-chr1:114445065..114452395,18	MCF-7	breast:
16	chr1:114300040..114303354-chr1:114351974..114356702,9	MCF-7	breast:
17	chr1:114353223..114356831-chr1:115298921..115302043,5	MCF-7	breast:
18	chr1:114352743..114357488-chr1:114365626..114369516,6	MCF-7	breast:
19	chr1:114298167..114305255-chr1:114351008..114356451,27	MCF-7	breast:
20	chr1:114328778..114330524-chr1:114356002..114358094,2	K562	blood:
21	chr1:114299507..114303267-chr1:114354438..114356409,4	K562	blood:
22	chr1:114352067..114356642-chr1:114470131..114477025,16	MCF-7	breast:

No data

Variant related genes	Relation type
RSBN1	TF binding region
ENSG00000163349	Chromatin interaction
ENSG00000134262	Chromatin interaction
ENSG00000155380	Chromatin interaction
ENSG00000009307	Chromatin interaction
ENSG00000231128	Chromatin interaction
ENSG00000235527	Chromatin interaction
ENSG00000118655	Chromatin interaction
ENSG00000124171	Chromatin interaction
ENSG00000197323	Chromatin interaction
ENSG00000116793	Chromatin interaction
ENSG00000081019	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10858016	0.87[ASN][1000 genomes]
rs1111695	0.87[ASN][1000 genomes]
rs1217375	0.82[AFR][1000 genomes]
rs1217378	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1217379	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1217385	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1217404	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1217405	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217406	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1217409	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217418	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217419	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1217420	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1230682	0.97[ASN][1000 genomes]
rs1230686	0.97[ASN][1000 genomes]
rs1235005	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1310182	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1539437	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2273758	0.93[ASN][1000 genomes]
rs2476599	0.82[AFR][1000 genomes]
rs2476600	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2476604	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2797414	0.97[ASN][1000 genomes]
rs2797416	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789598	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3789600	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4991898	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6537798	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6665194	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6672018	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7555634	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556622	0.87[ASN][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	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription 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 miRNA target site	96 gene(s)	inside rSNPs	diseases
2	nsv831093	chr1:114254167-114378235	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	esv1826178	chr1:114331645-114471583	Strong transcription Flanking Active TSS Active TSS Weak transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	esv1842398	chr1:114331645-114471583	Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
5	esv1848035	chr1:114331645-114471583	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1217411	PTPN22	cis	brain	BrainEAC

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114352400-114356200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr1:114355000-114401000	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:114355000-114401000	Weak transcription	Spleen	Spleen
4	chr1:114355400-114356200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
5	chr1:114355600-114356200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:114355600-114356200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:114355600-114357000	Weak transcription	Gastric	stomach
8	chr1:114355600-114358600	Weak transcription	GM12878-XiMat	blood
9	chr1:114355800-114356200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr1:114355800-114356200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:114355800-114356200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr1:114355800-114356200	Enhancers	Brain Germinal Matrix	brain
13	chr1:114355800-114356200	Enhancers	Left Ventricle	heart
14	chr1:114355800-114356200	Enhancers	Pancreas	Pancrea
15	chr1:114355800-114356400	Enhancers	Dnd41	blood
16	chr1:114355800-114356400	Enhancers	K562	blood
17	chr1:114355800-114357200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:114355800-114357200	Weak transcription	Monocytes-CD14+_RO01746	blood
19	chr1:114355800-114358200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
20	chr1:114355800-114361200	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:114355800-114364200	Weak transcription	Primary T cells from cord blood	blood
22	chr1:114355800-114364400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:114355800-114376600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
24	chr1:114355800-114376800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr1:114355800-114397400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr1:114355800-114413000	Weak transcription	Rectal Mucosa Donor 31	rectum
27	chr1:114356000-114356200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr1:114356000-114356200	Enhancers	Small Intestine	intestine
29	chr1:114356000-114357800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr1:114356000-114357800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr1:114356000-114358400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr1:114356000-114358600	Weak transcription	Primary T cells fromperipheralblood	blood
33	chr1:114356000-114358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr1:114356000-114359800	Weak transcription	Primary B cells from cord blood	blood
35	chr1:114356000-114360800	Weak transcription	Fetal Thymus	thymus
36	chr1:114356000-114362200	Weak transcription	Primary B cells from peripheral blood	blood
37	chr1:114356000-114364000	Weak transcription	Thymus	Thymus
38	chr1:114356000-114370200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr1:114356000-114370600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr1:114356000-114376800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:114356000-114377400	Strong transcription	Primary neutrophils fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links