Variant report

Variant	rs2525050
Chromosome Location	chr12:48196097-48196098
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:28)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:28 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr12:48196040-48196190	HVMF	connective:	n/a	n/a
2	ZNF143	chr12:48196079-48196390	H1-hESC	embryonic stem cell:	n/a	n/a
3	SIN3AK20	chr12:48196000-48196869	MCF-7	breast:	n/a	n/a
4	CTCF	chr12:48196080-48196230	HRE	kidney:	n/a	n/a
5	GATA2	chr12:48196064-48196833	SH-SY5Y	brain:	n/a	chr12:48196396-48196404
6	CTCF	chr12:48196080-48196230	BE2_C	brain:	n/a	n/a
7	CTCF	chr12:48196090-48196351	GM12878	blood:	n/a	n/a
8	CTCF	chr12:48196094-48196351	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr12:48195569-48196594	HUVEC	blood vessel:	n/a	n/a
10	GATA3	chr12:48196009-48196906	MCF-7	breast:	n/a	chr12:48196396-48196404
11	CTCF	chr12:48196040-48196330	HMEC	breast:	n/a	n/a
12	POLR2A	chr12:48195295-48197895	ECC-1	luminal epithelium:	n/a	n/a
13	GATA3	chr12:48196089-48196712	SK-N-SH	brain:	n/a	chr12:48196396-48196404
14	CTCF	chr12:48196033-48196509	K562	blood:	n/a	chr12:48196360-48196373
15	CTCF	chr12:48196072-48196366	K562	blood:	n/a	n/a
16	GATA3	chr12:48196073-48196977	MCF-7	breast:	n/a	chr12:48196396-48196404
17	CTCF	chr12:48196059-48196424	H1-hESC	embryonic stem cell:	n/a	chr12:48196360-48196373
18	POLR2A	chr12:48195924-48196439	K562	blood:	n/a	n/a
19	GATA3	chr12:48195974-48197135	MCF-7	breast:	n/a	chr12:48196396-48196404
20	CTCF	chr12:48196060-48196330	GM12870	blood:	n/a	n/a
21	CTCF	chr12:48196029-48196458	H1-hESC	embryonic stem cell:	n/a	chr12:48196360-48196373
22	ZBTB7A	chr12:48196064-48196353	K562	blood:	n/a	n/a
23	POLR2A	chr12:48195892-48196614	Hela-S3	cervix:	n/a	n/a
24	CTCF	chr12:48196080-48196230	GM12864	blood:	n/a	n/a
25	CTCF	chr12:48196040-48196190	HCM	heart:	n/a	n/a
26	NR2F2	chr12:48195947-48197028	MCF-7	breast:	n/a	n/a
27	CTCF	chr12:48196060-48196210	WI-38	lung:	n/a	n/a
28	NR2F2	chr12:48196085-48196875	MCF-7	breast:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:48194186..48196955-chr12:48205034..48206864,2	K562	blood:
2	chr12:48188175..48191554-chr12:48193435..48196727,4	K562	blood:
3	chr12:48166395..48169503-chr12:48195683..48198388,3	MCF-7	breast:
4	chr12:48178200..48181079-chr12:48195107..48197877,2	K562	blood:
5	chr12:48194186..48197622-chr12:48205034..48208393,5	K562	blood:
6	chr12:48194244..48196196-chr12:48197765..48200382,2	MCF-7	breast:
7	chr12:48189801..48192415-chr12:48195227..48196888,2	K562	blood:

No data

Variant related genes	Relation type
HDAC7	TF binding region
ENSG00000211584	Chromatin interaction
ENSG00000061273	Chromatin interaction
ENSG00000268069	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11574041	1.00[EUR][1000 genomes]
rs2853560	1.00[AMR][1000 genomes]
rs41272781	1.00[EUR][1000 genomes]
rs58436504	1.00[EUR][1000 genomes]
rs61048429	1.00[EUR][1000 genomes]
rs61412033	1.00[AMR][1000 genomes]
rs7974905	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1051941	chr12:48114026-48233128	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
2	nsv541487	chr12:48114026-48233128	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
3	nsv1036804	chr12:48114026-48287048	Enhancers Genic enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
4	nsv524967	chr12:48119562-48215180	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv899059	chr12:48129344-48215180	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
6	nsv1052034	chr12:48146633-48287048	Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
7	nsv899060	chr12:48180508-48231430	Enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
8	esv3693398	chr12:48186738-48215749	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	57 gene(s)	inside rSNPs	diseases
9	nsv1048466	chr12:48195350-48262541	Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
10	nsv541488	chr12:48195350-48262541	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:48178600-48199200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr12:48179800-48201000	Weak transcription	Dnd41	blood
3	chr12:48181200-48199800	Strong transcription	Fetal Intestine Small	intestine
4	chr12:48182000-48206400	Weak transcription	HepG2	liver
5	chr12:48182400-48202000	Weak transcription	Fetal Brain Male	brain
6	chr12:48183000-48204000	Weak transcription	Fetal Kidney	kidney
7	chr12:48188600-48196600	Weak transcription	K562	blood
8	chr12:48189000-48201000	Weak transcription	NH-A	brain
9	chr12:48190800-48201400	Genic enhancers	Fetal Thymus	thymus
10	chr12:48191000-48197200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr12:48191000-48201200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:48191400-48197200	Enhancers	Brain Angular Gyrus	brain
13	chr12:48191400-48200000	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr12:48191400-48200200	Genic enhancers	Primary T cells fromperipheralblood	blood
15	chr12:48191400-48200600	Genic enhancers	Fetal Muscle Trunk	muscle
16	chr12:48191400-48201400	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr12:48191400-48202800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr12:48191600-48196800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr12:48191600-48201600	Genic enhancers	Thymus	Thymus
20	chr12:48191800-48196200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr12:48192000-48196800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr12:48192000-48198000	Enhancers	Brain Anterior Caudate	brain
23	chr12:48192200-48200200	Genic enhancers	Lung	lung
24	chr12:48192400-48196200	Genic enhancers	Primary B cells from peripheral blood	blood
25	chr12:48192400-48196800	Enhancers	Psoas Muscle	Psoas
26	chr12:48192400-48201000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr12:48192400-48201600	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr12:48192400-48203200	Enhancers	Right Atrium	heart
29	chr12:48192600-48196200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr12:48192600-48196400	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr12:48192600-48197000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr12:48192600-48198000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:48192600-48198800	Weak transcription	Fetal Brain Female	brain
34	chr12:48192600-48201400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
35	chr12:48192800-48197600	Enhancers	Left Ventricle	heart
36	chr12:48192800-48200200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr12:48192800-48200200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
38	chr12:48193000-48197200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:48193000-48200400	Genic enhancers	Fetal Muscle Leg	muscle
40	chr12:48193200-48197200	Enhancers	Colon Smooth Muscle	Colon
41	chr12:48193200-48198000	Enhancers	Duodenum Mucosa	Duodenum
42	chr12:48193200-48200000	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr12:48193200-48200200	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr12:48193200-48200200	Enhancers	Pancreas	Pancrea
45	chr12:48193400-48197600	Enhancers	Placenta	Placenta
46	chr12:48193400-48197800	Enhancers	NHDF-Ad	bronchial
47	chr12:48193400-48198200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr12:48193400-48200200	Enhancers	Brain Substantia Nigra	brain
49	chr12:48193400-48203000	Enhancers	Fetal Heart	heart
50	chr12:48193400-48205000	Weak transcription	Brain Germinal Matrix	brain

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