Variant report

Variant	rs28661251
Chromosome Location	chr17:38024331-38024332
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	EGR1	chr17:38024249-38024514	GM12878	blood:	n/a	chr17:38024413-38024423 chr17:38024412-38024425 chr17:38024413-38024422 chr17:38024412-38024425 chr17:38024411-38024425 chr17:38024367-38024377 chr17:38024411-38024426 chr17:38024412-38024425 chr17:38024412-38024422 chr17:38024409-38024423 chr17:38024410-38024420 chr17:38024365-38024378 chr17:38024438-38024447 chr17:38024412-38024425
2	MEF2C	chr17:38023065-38024527	GM12878	blood:	n/a	chr17:38023410-38023431 chr17:38023488-38023496
3	POLR2A	chr17:38022336-38024945	GM18505	blood:	n/a	n/a
4	MAX	chr17:38024058-38024697	H1-hESC	embryonic stem cell:	n/a	chr17:38024367-38024376
5	NFATC1	chr17:38023099-38024499	GM12878	blood:	n/a	n/a
6	BCL3	chr17:38023200-38024490	GM12878	blood:	n/a	chr17:38023905-38023914 chr17:38024227-38024236 chr17:38024411-38024424
7	YY1	chr17:38023824-38024553	GM12891	blood:	n/a	chr17:38024411-38024420
8	BCLAF1	chr17:38023108-38024567	GM12878	blood:	n/a	chr17:38023905-38023914 chr17:38024227-38024236 chr17:38024411-38024424
9	TBL1XR1	chr17:38023178-38024491	GM12878	blood:	n/a	n/a
10	ATF2	chr17:38022555-38024496	GM12878	blood:	n/a	n/a
11	YY1	chr17:38023401-38024601	GM12878	blood:	n/a	chr17:38024411-38024420
12	MAX	chr17:38024167-38024564	H1-hESC	embryonic stem cell:	n/a	chr17:38024367-38024376
13	RELA	chr17:38023254-38024573	GM18951	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
14	NFIC	chr17:38022926-38024693	GM12878	blood:	n/a	n/a
15	BHLHE40	chr17:38023169-38024618	GM12878	blood:	n/a	chr17:38024360-38024376 chr17:38024076-38024089 chr17:38024072-38024093
16	E2F6	chr17:38024145-38024703	H1-hESC	embryonic stem cell:	n/a	chr17:38024313-38024327 chr17:38024316-38024323 chr17:38024341-38024348 chr17:38024316-38024323 chr17:38024316-38024323 chr17:38024341-38024348 chr17:38024341-38024348 chr17:38024312-38024324 chr17:38024340-38024349 chr17:38024411-38024420
17	POLR2A	chr17:38023225-38024718	GM15510	blood:	n/a	n/a
18	RELA	chr17:38023169-38024357	GM12878	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
19	TCF3	chr17:38024201-38024647	GM12878	blood:	n/a	n/a
20	POLR2A	chr17:38023153-38024680	GM12891	blood:	n/a	n/a
21	STAT5A	chr17:38023077-38024790	GM12878	blood:	n/a	chr17:38024274-38024282 chr17:38024733-38024745 chr17:38024106-38024118
22	RELA	chr17:38023172-38024484	GM18505	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
23	MTA3	chr17:38022147-38025265	GM12878	blood:	n/a	n/a
24	PAX5	chr17:38023413-38024704	GM12878	blood:	n/a	n/a
25	PAX5	chr17:38023173-38024641	GM12878	blood:	n/a	n/a
26	EGR1	chr17:38024217-38024546	GM12878	blood:	n/a	chr17:38024413-38024423 chr17:38024412-38024425 chr17:38024413-38024422 chr17:38024412-38024425 chr17:38024411-38024425 chr17:38024367-38024377 chr17:38024411-38024426 chr17:38024412-38024425 chr17:38024412-38024422 chr17:38024409-38024423 chr17:38024410-38024420 chr17:38024365-38024378 chr17:38024438-38024447 chr17:38024412-38024425
27	RUNX3	chr17:38023032-38024461	GM12878	blood:	n/a	n/a
28	POLR2A	chr17:38023065-38024781	GM12892	blood:	n/a	n/a
29	RELA	chr17:38023213-38024514	GM15510	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
30	RELA	chr17:38023075-38024469	GM19193	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
31	POLR2A	chr17:38023143-38024679	GM12891	blood:	n/a	n/a
32	NFIC	chr17:38023081-38024487	GM12878	blood:	n/a	n/a
33	POLR2A	chr17:38023052-38024517	GM12878	blood:	n/a	n/a
34	MAX	chr17:38023337-38024660	GM12878	blood:	n/a	chr17:38024367-38024376
35	TCF12	chr17:38024274-38024546	GM12878	blood:	n/a	n/a
36	POLR2A	chr17:38023115-38024854	GM12892	blood:	n/a	n/a
37	USF2	chr17:38023895-38024348	GM12878	blood:	n/a	chr17:38024076-38024089 chr17:38024072-38024093
38	BATF	chr17:38023205-38024346	GM12878	blood:	n/a	chr17:38023358-38023368
39	POLR2A	chr17:38023137-38024880	GM12892	blood:	n/a	n/a
40	POLR2A	chr17:38023146-38024610	GM12891	blood:	n/a	n/a
41	MTA3	chr17:38023069-38024733	GM12878	blood:	n/a	n/a
42	IRF4	chr17:38023157-38024339	GM12878	blood:	n/a	chr17:38023493-38023507
43	CEBPB	chr17:38022400-38024352	GM12878	blood:	n/a	n/a
44	POLR2A	chr17:38023125-38024730	GM19099	blood:	n/a	n/a
45	SP1	chr17:38023278-38024630	GM12878	blood:	n/a	chr17:38024410-38024420 chr17:38024410-38024419 chr17:38024410-38024420 chr17:38024409-38024421 chr17:38024411-38024420 chr17:38024409-38024421 chr17:38024410-38024419
46	TAF1	chr17:38024168-38024448	GM12892	blood:	n/a	n/a
47	YY1	chr17:38023416-38024655	GM12892	blood:	n/a	chr17:38024411-38024420
48	STAT5A	chr17:38023157-38024589	GM12878	blood:	n/a	chr17:38024274-38024282 chr17:38024106-38024118
49	RELA	chr17:38023161-38024571	GM12892	blood:	n/a	chr17:38024052-38024061 chr17:38024052-38024061
50	ATF2	chr17:38023105-38024425	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38016485..38022109-chr17:38022345..38027890,7	K562	blood:

Variant related genes	Relation type
IKZF3	TF binding region
ZPBP2	TF binding region
ENSG00000161405	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs13341681	1.00[AMR][1000 genomes]
rs13380812	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28407584	1.00[AMR][1000 genomes]
rs28409251	1.00[AMR][1000 genomes]
rs28432878	1.00[AMR][1000 genomes]
rs28464000	1.00[AMR][1000 genomes]
rs28494476	1.00[AMR][1000 genomes]
rs28498893	1.00[AMR][1000 genomes]
rs28505218	1.00[AMR][1000 genomes]
rs28627663	1.00[AMR][1000 genomes]
rs28673180	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28714172	1.00[AMR][1000 genomes]
rs28882824	1.00[AMR][1000 genomes]
rs61737968	1.00[AMR][1000 genomes]
rs62065168	1.00[AMR][1000 genomes]
rs62065210	1.00[AMR][1000 genomes]
rs9890508	1.00[AMR][1000 genomes]
rs9890819	1.00[AMR][1000 genomes]
rs9893628	1.00[AMR][1000 genomes]
rs9893933	1.00[AMR][1000 genomes]
rs9895237	1.00[AMR][1000 genomes]
rs9896961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9897451	1.00[AMR][1000 genomes]
rs9897847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9899977	1.00[AMR][1000 genomes]
rs9900885	1.00[AMR][1000 genomes]
rs9911163	1.00[AMR][1000 genomes]
rs9913746	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9914556	1.00[AMR][1000 genomes]
rs9916301	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064787	chr17:37892843-38054410	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv543342	chr17:37892843-38054410	Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
3	esv1795575	chr17:37974075-38041762	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38022200-38025200	Flanking Active TSS	GM12878-XiMat	blood
2	chr17:38022400-38025200	Enhancers	Primary B cells from cord blood	blood
3	chr17:38023200-38024400	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
4	chr17:38023200-38024400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
5	chr17:38023200-38024600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr17:38023400-38024400	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr17:38023400-38024800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
8	chr17:38023400-38024800	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
9	chr17:38023400-38024800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
10	chr17:38023600-38024800	Flanking Active TSS	Primary B cells from peripheral blood	blood
11	chr17:38023600-38024800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr17:38023600-38025000	ZNF genes & repeats	Esophagus	oesophagus
13	chr17:38023800-38024600	Flanking Bivalent TSS/Enh	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:38023800-38024600	ZNF genes & repeats	Pancreas	Pancrea
15	chr17:38024000-38024400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
16	chr17:38024000-38024600	Bivalent/Poised TSS	Colonic Mucosa	Colon
17	chr17:38024000-38024600	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
18	chr17:38024000-38024600	Bivalent/Poised TSS	Thymus	Thymus
19	chr17:38024000-38024800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr17:38024200-38024400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
21	chr17:38024200-38024400	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr17:38024200-38024400	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
23	chr17:38024200-38024400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr17:38024200-38024400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr17:38024200-38024400	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr17:38024200-38024400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr17:38024200-38024400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
28	chr17:38024200-38024400	Bivalent/Poised TSS	Right Atrium	heart
29	chr17:38024200-38024400	Bivalent Enhancer	Small Intestine	intestine
30	chr17:38024200-38024600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr17:38024200-38024600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
32	chr17:38024200-38024600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr17:38024200-38024600	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr17:38024200-38024600	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
35	chr17:38024200-38024600	Active TSS	Duodenum Mucosa	Duodenum
36	chr17:38024200-38024600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
37	chr17:38024200-38024600	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
38	chr17:38024200-38024800	ZNF genes & repeats	Spleen	Spleen
39	chr17:38024200-38025000	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell

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