Variant report

Variant	rs11502798
Chromosome Location	chr12:9826064-9826065
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:72)
CpG islands
(count:0)
Chromatin interactive
region (count:1)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:72 , 50 per page) page: 1 2

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	NR2F2	chr12:9825970-9826580	MCF-7	breast:	n/a	n/a
2	NR2F2	chr12:9825946-9826772	K562	blood:	n/a	n/a
3	CHD2	chr12:9826035-9826745	GM12878	blood:	n/a	n/a
4	STAT5A	chr12:9825984-9826704	K562	blood:	n/a	n/a
5	POLR2A	chr12:9825672-9827322	GM18951	blood:	n/a	n/a
6	POLR2A	chr12:9825909-9827311	GM12892	blood:	n/a	n/a
7	FOXM1	chr12:9826014-9827318	GM12878	blood:	n/a	n/a
8	BACH1	chr12:9826040-9826692	K562	blood:	n/a	n/a
9	FOSL2	chr12:9825995-9826739	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr12:9826038-9827475	GM15510	blood:	n/a	n/a
11	POLR2A	chr12:9822858-9827605	GM12891	blood:	n/a	n/a
12	MTA3	chr12:9825386-9827372	GM12878	blood:	n/a	n/a
13	PAX5	chr12:9825948-9826784	GM12878	blood:	n/a	n/a
14	TEAD4	chr12:9825933-9826691	K562	blood:	n/a	n/a
15	BCLAF1	chr12:9825980-9826744	GM12878	blood:	n/a	n/a
16	MAFK	chr12:9826063-9826699	K562	blood:	n/a	n/a
17	POLR2A	chr12:9825775-9827205	GM12892	blood:	n/a	n/a
18	REST	chr12:9826039-9826731	K562	blood:	n/a	n/a
19	EP300	chr12:9825982-9827123	K562	blood:	n/a	n/a
20	EP300	chr12:9826000-9826910	SK-N-SH	brain:	n/a	n/a
21	NFIC	chr12:9825988-9826811	SK-N-SH	brain:	n/a	n/a
22	TEAD4	chr12:9825964-9826749	K562	blood:	n/a	n/a
23	POLR2A	chr12:9825908-9826867	K562	blood:	n/a	n/a
24	POLR2A	chr12:9825851-9827196	GM19193	blood:	n/a	n/a
25	CBX3	chr12:9826048-9826757	K562	blood:	n/a	n/a
26	ELF1	chr12:9825982-9827291	GM12878	blood:	n/a	n/a
27	POLR2A	chr12:9823968-9827308	GM12892	blood:	n/a	n/a
28	MAZ	chr12:9825979-9827283	IMR90	lung:	n/a	n/a
29	POLR2A	chr12:9825691-9827317	GM18526	blood:	n/a	n/a
30	TCF7L2	chr12:9825869-9826217	MCF-7	breast:	n/a	n/a
31	JUND	chr12:9826037-9826732	K562	blood:	n/a	n/a
32	RELA	chr12:9825991-9827267	GM15510	blood:	n/a	n/a
33	POLR2A	chr12:9822835-9827266	GM12892	blood:	n/a	n/a
34	POLR2A	chr12:9824036-9827274	GM12878	blood:	n/a	n/a
35	RELA	chr12:9826020-9826567	GM10847	blood:	n/a	n/a
36	MAFF	chr12:9826022-9826700	K562	blood:	n/a	n/a
37	ARID3A	chr12:9825995-9826394	K562	blood:	n/a	n/a
38	NFATC1	chr12:9826006-9826764	GM12878	blood:	n/a	n/a
39	RUNX3	chr12:9825904-9827225	GM12878	blood:	n/a	n/a
40	POLR2A	chr12:9826059-9827121	GM12878	blood:	n/a	n/a
41	RELA	chr12:9825916-9827190	GM19193	blood:	n/a	n/a
42	RELA	chr12:9825751-9827270	GM18951	blood:	n/a	n/a
43	TBL1XR1	chr12:9825850-9826691	GM12878	blood:	n/a	n/a
44	TRIM28	chr12:9826012-9826518	K562	blood:	n/a	n/a
45	POLR2A	chr12:9825418-9827310	GM19099	blood:	n/a	n/a
46	GATA3	chr12:9826021-9826910	SK-N-SH	brain:	n/a	n/a
47	JUN	chr12:9825463-9827142	K562	blood:	n/a	n/a
48	TCF12	chr12:9825960-9826897	SK-N-SH	brain:	n/a	n/a
49	RCOR1	chr12:9826043-9826737	K562	blood:	n/a	n/a
50	POLR2A	chr12:9821389-9827321	Raji	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:9799292..9802850-chr12:9823422..9827161,3	MCF-7	breast:

No data

Variant related genes	Relation type
CLEC2D	TF binding region
ENSG00000256594	Chromatin interaction
ENSG00000256442	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11052369	1.00[AMR][1000 genomes]
rs11052389	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11052412	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11052468	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11052537	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11052550	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1118223	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11502800	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12301473	1.00[AMR][1000 genomes]
rs12302794	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12312233	1.00[AMR][1000 genomes]
rs12316684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12318225	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9668079	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv427903	chr12:9371593-9830668	Active TSS Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	esv2758293	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
3	esv2759878	chr12:9371595-9923529	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
4	esv1821732	chr12:9560087-9830668	Strong transcription Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
5	esv1823760	chr12:9560087-9830668	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv428271	chr12:9560087-9830668	Enhancers Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:114 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9802400-9849800	Weak transcription	Pancreas	Pancrea
2	chr12:9803600-9826200	Weak transcription	Esophagus	oesophagus
3	chr12:9807600-9847200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr12:9813000-9826200	Weak transcription	Brain Anterior Caudate	brain
5	chr12:9813000-9826200	Weak transcription	Gastric	stomach
6	chr12:9815000-9826200	Weak transcription	Colonic Mucosa	Colon
7	chr12:9815000-9826200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr12:9815000-9826400	Weak transcription	Fetal Intestine Small	intestine
9	chr12:9815200-9826200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr12:9815200-9828400	Weak transcription	Liver	Liver
11	chr12:9815200-9840600	Weak transcription	Fetal Brain Male	brain
12	chr12:9815200-9841600	Weak transcription	Fetal Kidney	kidney
13	chr12:9815600-9833800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:9816200-9832600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:9816200-9840600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr12:9817200-9837800	Weak transcription	Aorta	Aorta
17	chr12:9817600-9826400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr12:9818000-9826200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr12:9818000-9839200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr12:9818000-9839800	Weak transcription	Ovary	ovary
21	chr12:9818000-9840000	Weak transcription	Fetal Intestine Large	intestine
22	chr12:9818000-9849800	Weak transcription	Brain Germinal Matrix	brain
23	chr12:9818200-9826200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
24	chr12:9818200-9826400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr12:9818200-9828600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
26	chr12:9818200-9840000	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr12:9822400-9827200	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
28	chr12:9823000-9829800	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
29	chr12:9823600-9826600	Weak transcription	Rectal Smooth Muscle	rectum
30	chr12:9824200-9827400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
31	chr12:9824200-9827800	Flanking Active TSS	Primary T cells from cord blood	blood
32	chr12:9824200-9828200	Transcr. at gene 5' and 3'	Primary B cells from cord blood	blood
33	chr12:9824200-9828200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
34	chr12:9824400-9832600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr12:9824600-9827200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:9824600-9827200	Transcr. at gene 5' and 3'	Primary T regulatory cells fromperipheralblood	blood
37	chr12:9824800-9827200	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr12:9825000-9826200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr12:9825200-9827200	Enhancers	Placenta Amnion	Placenta Amnion
40	chr12:9825400-9826200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:9825400-9827200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
42	chr12:9825400-9827200	Enhancers	Fetal Heart	heart
43	chr12:9825600-9826200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr12:9825600-9826400	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr12:9825600-9826400	Enhancers	NHEK	skin
46	chr12:9825600-9826400	Enhancers	Osteobl	bone
47	chr12:9825600-9826600	Enhancers	HepG2	liver
48	chr12:9825600-9826800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
49	chr12:9825600-9826800	Enhancers	Monocytes-CD14+_RO01746	blood
50	chr12:9825600-9827000	Enhancers	HUES6 Cell Line	embryonic stem cell

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