Variant report

Variant	rs72921042
Chromosome Location	chr2:39457087-39457088
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	CEBPB	chr2:39456998-39457225	K562	blood:	n/a	chr2:39457135-39457148
2	CTCF	chr2:39457027-39457267	T-47D	breast:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
3	CTCF	chr2:39456899-39457391	GM12878	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
4	CTCF	chr2:39457080-39457230	HCPEpiC	choroid plexus:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
5	GTF2F1	chr2:39457081-39457242	H1-hESC	embryonic stem cell:	n/a	n/a
6	FOS	chr2:39457007-39457297	MCF10A-Er-Src	breast:	n/a	n/a
7	CTCF	chr2:39457006-39457318	K562	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
8	CTCF	chr2:39457058-39457307	HepG2	liver:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
9	ARID3A	chr2:39456608-39457299	HepG2	liver:	n/a	n/a
10	CEBPB	chr2:39456942-39457341	K562	blood:	n/a	chr2:39457135-39457148
11	CTCF	chr2:39457080-39457230	HPAF	blood vessel:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
12	RAD21	chr2:39456822-39457316	A549	lung:	n/a	chr2:39457168-39457187 chr2:39457177-39457186
13	CTCF	chr2:39457086-39457291	ProgFib	skin:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
14	EGR1	chr2:39456995-39457322	K562	blood:	n/a	n/a
15	TBP	chr2:39457023-39457418	K562	blood:	n/a	n/a
16	CEBPB	chr2:39456863-39457326	K562	blood:	n/a	chr2:39457135-39457148
17	CTCF	chr2:39457080-39457230	GM12875	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
18	EBF1	chr2:39457005-39457223	GM12878	blood:	n/a	n/a
19	FOXA1	chr2:39456987-39457259	T-47D	breast:	n/a	n/a
20	RAD21	chr2:39456952-39457425	H1-hESC	embryonic stem cell:	n/a	chr2:39457168-39457187 chr2:39457177-39457186
21	CTCF	chr2:39457080-39457230	HPF	lung:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
22	CTCF	chr2:39457080-39457230	SK-N-SH_RA	brain:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
23	RAD21	chr2:39456904-39457333	GM12878	blood:	n/a	chr2:39457168-39457187 chr2:39457177-39457186
24	CTCF	chr2:39457014-39457313	K562	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
25	FOS	chr2:39457032-39457272	MCF10A-Er-Src	breast:	n/a	n/a
26	CTCF	chr2:39457059-39457354	Medullo	brain:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
27	MYC	chr2:39457014-39457311	MCF10A-Er-Src	breast:	n/a	n/a
28	CEBPB	chr2:39456945-39457337	IMR90	lung:	n/a	chr2:39457135-39457148
29	HCFC1	chr2:39456933-39457241	K562	blood:	n/a	n/a
30	RAD21	chr2:39456762-39457415	HepG2	liver:	n/a	chr2:39457168-39457187 chr2:39457177-39457186
31	RAD21	chr2:39456957-39457432	ECC-1	luminal epithelium:	n/a	chr2:39457168-39457187 chr2:39457177-39457186
32	CTCF	chr2:39456979-39457326	MCF-7	breast:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
33	CTCF	chr2:39457080-39457230	GM12874	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
34	CEBPB	chr2:39456980-39457348	H1-hESC	embryonic stem cell:	n/a	chr2:39457135-39457148
35	RFX5	chr2:39456971-39457270	K562	blood:	n/a	n/a
36	CEBPB	chr2:39456798-39457462	MCF-7	breast:	n/a	chr2:39457135-39457148
37	CTCF	chr2:39457080-39457230	BJ	skin:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
38	CTCF	chr2:39457080-39457230	AG10803	skin:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
39	CTCF	chr2:39457080-39457230	AG04449	skin:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
40	TBP	chr2:39457010-39457420	HepG2	liver:	n/a	n/a
41	CTCF	chr2:39457080-39457230	GM12865	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
42	CTCF	chr2:39457080-39457230	GM12868	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
43	FOS	chr2:39457023-39457305	MCF10A-Er-Src	breast:	n/a	n/a
44	CTCF	chr2:39457080-39457230	AG09309	skin:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185
45	E2F4	chr2:39457026-39457318	MCF10A-Er-Src	breast:	n/a	n/a
46	RAD21	chr2:39456562-39457572	SK-N-SH	brain:	n/a	chr2:39457168-39457187 chr2:39457177-39457186
47	MBD4	chr2:39456868-39457419	HepG2	liver:	n/a	n/a
48	TBL1XR1	chr2:39456984-39457330	K562	blood:	n/a	n/a
49	SMC3	chr2:39456941-39457387	GM12878	blood:	n/a	chr2:39457172-39457186
50	CTCF	chr2:39457053-39457317	K562	blood:	n/a	chr2:39457165-39457186 chr2:39457170-39457188 chr2:39457176-39457185

No.	Distal block	Cell Line	Cell type
1	chr2:39262956..39263678-chr2:39457038..39457575,2	MCF-7	breast:
2	chr2:39286437..39287460-chr2:39456992..39457994,4	MCF-7	breast:
3	chr2:39346582..39349686-chr2:39454756..39458494,4	MCF-7	breast:
4	chr2:39346444..39348213-chr2:39455953..39458743,3	MCF-7	breast:

Variant related genes	Relation type
CDKL4	TF binding region
ENSG00000115904	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs17023556	1.00[AMR][1000 genomes]
rs56755150	1.00[AMR][1000 genomes]
rs56838255	1.00[AMR][1000 genomes]
rs57447134	1.00[AMR][1000 genomes]
rs57604567	1.00[AMR][1000 genomes]
rs58351262	1.00[AMR][1000 genomes]
rs58532689	1.00[AMR][1000 genomes]
rs59788679	1.00[AMR][1000 genomes]
rs60025924	1.00[AMR][1000 genomes]
rs60938752	1.00[AMR][1000 genomes]
rs72921035	1.00[AMR][1000 genomes]
rs72921046	1.00[AMR][1000 genomes]
rs72921048	1.00[AMR][1000 genomes]
rs72921055	1.00[AMR][1000 genomes]
rs72921056	1.00[AMR][1000 genomes]
rs72921062	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72921063	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72923480	1.00[AMR][1000 genomes]
rs72923481	1.00[AMR][1000 genomes]
rs72923484	1.00[AMR][1000 genomes]
rs72923490	1.00[AMR][1000 genomes]
rs72925230	1.00[AMR][1000 genomes]
rs72927490	1.00[AMR][1000 genomes]
rs7608216	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv873885	chr2:39200198-39573521	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1010874	chr2:39255376-39604535	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	nsv535649	chr2:39255376-39604535	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv531346	chr2:39263225-39606367	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
5	nsv533348	chr2:39264345-39596169	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv1014520	chr2:39270598-39596299	Enhancers Active TSS Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
7	nsv535650	chr2:39270598-39596299	Enhancers Active TSS Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
8	nsv1009379	chr2:39271472-39604535	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
9	nsv581493	chr2:39277851-39547575	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
10	nsv581494	chr2:39277851-39626388	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
11	nsv533456	chr2:39281834-39596298	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
12	nsv581495	chr2:39282079-39475205	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
13	nsv1000658	chr2:39374206-39466374	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	esv1832414	chr2:39385155-39588797	Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	esv1827292	chr2:39385155-39675339	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
16	esv1812828	chr2:39396457-39675339	Flanking Active TSS Strong transcription Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
17	nsv833847	chr2:39410762-39604640	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	nsv533445	chr2:39412970-39605266	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
19	esv1830024	chr2:39440552-39588797	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:39423400-39470800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:39429800-39459600	Weak transcription	HSMM	muscle
3	chr2:39449200-39477600	Weak transcription	HSMMtube	muscle
4	chr2:39455400-39470600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:39455800-39457400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:39455800-39472200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr2:39456000-39457200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
8	chr2:39456000-39457200	Enhancers	Fetal Heart	heart
9	chr2:39456000-39457600	Enhancers	HUVEC	blood vessel
10	chr2:39456000-39457800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:39456000-39459400	Weak transcription	Osteobl	bone
12	chr2:39456000-39472000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr2:39456200-39457200	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr2:39456200-39457200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:39456200-39457200	Enhancers	Fetal Intestine Large	intestine
16	chr2:39456200-39460400	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr2:39456200-39475600	Weak transcription	NHDF-Ad	bronchial
18	chr2:39456400-39457200	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr2:39456400-39457200	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr2:39456400-39457200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr2:39456400-39461400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr2:39456600-39457200	Enhancers	Colon Smooth Muscle	Colon
23	chr2:39456800-39457600	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:39456800-39457600	Enhancers	HepG2	liver
25	chr2:39457000-39457200	Enhancers	A549	lung
26	chr2:39457000-39457800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr2:39457000-39460400	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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