Variant report

Variant	rs6711817
Chromosome Location	chr2:190538952-190538953
allele	C/G
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	POLR2A	chr2:190538889-190539761	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:190538049-190539923	GM12891	blood:	n/a	n/a
3	FOXA1	chr2:190538917-190539532	HepG2	liver:	n/a	n/a
4	ATF2	chr2:190538937-190539616	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:190538921-190539783	GM12892	blood:	n/a	n/a
6	CTCF	chr2:190538569-190539948	A549	lung:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
7	POLR2A	chr2:190536047-190539158	K562	blood:	n/a	n/a
8	POLR2A	chr2:190538947-190539755	GM12891	blood:	n/a	n/a
9	PML	chr2:190538715-190539878	GM12878	blood:	n/a	n/a
10	MYBL2	chr2:190538677-190539983	HepG2	liver:	n/a	n/a
11	CTCF	chr2:190538925-190539548	H1-hESC	embryonic stem cell:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
12	MAX	chr2:190538928-190539599	H1-hESC	embryonic stem cell:	n/a	n/a
13	TEAD4	chr2:190538873-190539605	HepG2	liver:	n/a	n/a
14	MAX	chr2:190538879-190539782	SK-N-SH	brain:	n/a	n/a
15	YY1	chr2:190538952-190539745	SK-N-SH_RA	brain:	n/a	chr2:190539188-190539202 chr2:190539193-190539202
16	NR2F2	chr2:190538948-190539632	MCF-7	breast:	n/a	n/a
17	TCF12	chr2:190538942-190539884	A549	lung:	n/a	n/a
18	POLR2A	chr2:190538814-190539845	GM12892	blood:	n/a	n/a
19	SIN3AK20	chr2:190538941-190539638	PANC-1	pancreas:	n/a	n/a
20	CTCF	chr2:190538840-190538990	GM12878	blood:	n/a	n/a
21	RELA	chr2:190538917-190539693	GM15510	blood:	n/a	n/a
22	STAT5A	chr2:190538841-190539857	GM12878	blood:	n/a	n/a
23	RFX5	chr2:190538790-190539793	HepG2	liver:	n/a	n/a
24	MAX	chr2:190538886-190539884	SK-N-SH	brain:	n/a	n/a
25	HA-E2F1	chr2:190538658-190539928	MCF-7	breast:	n/a	chr2:190539195-190539205
26	MTA3	chr2:190538761-190539866	GM12878	blood:	n/a	n/a
27	MYBL2	chr2:190538926-190540039	HepG2	liver:	n/a	n/a
28	MXI1	chr2:190538947-190539768	HepG2	liver:	n/a	n/a
29	MAX	chr2:190538871-190539784	MCF-7	breast:	n/a	n/a
30	HDAC2	chr2:190538920-190539701	MCF-7	breast:	n/a	n/a
31	GATA2	chr2:190538678-190539840	SH-SY5Y	brain:	n/a	n/a
32	TBP	chr2:190538762-190539860	H1-hESC	embryonic stem cell:	n/a	n/a
33	CREB1	chr2:190538835-190539922	HepG2	liver:	n/a	n/a
34	POLR2A	chr2:190538569-190539883	GM12878	blood:	n/a	n/a
35	POLR2A	chr2:190538780-190539902	HUVEC	blood vessel:	n/a	n/a
36	MBD4	chr2:190538832-190539933	HepG2	liver:	n/a	n/a
37	WRNIP1	chr2:190538744-190539145	GM12878	blood:	n/a	n/a
38	POLR2A	chr2:190538934-190539729	HUVEC	blood vessel:	n/a	n/a
39	USF2	chr2:190538939-190539295	HepG2	liver:	n/a	chr2:190539209-190539225
40	POLR2A	chr2:190538786-190539694	MCF10A-Er-Src	breast:	n/a	n/a
41	MAX	chr2:190538778-190539719	GM12878	blood:	n/a	n/a
42	RCOR1	chr2:190538866-190539821	HepG2	liver:	n/a	n/a
43	MAX	chr2:190538878-190539903	ECC-1	luminal epithelium:	n/a	n/a
44	MBD4	chr2:190538773-190539747	HepG2	liver:	n/a	n/a
45	CTCF	chr2:190538947-190539558	GM12878	blood:	n/a	chr2:190539196-190539212 chr2:190539195-190539208 chr2:190539198-190539211 chr2:190539195-190539213
46	MAX	chr2:190538854-190539876	ECC-1	luminal epithelium:	n/a	n/a
47	MXI1	chr2:190538758-190540045	SK-N-SH	brain:	n/a	n/a
48	POLR2A	chr2:190538952-190539977	H1-hESC	embryonic stem cell:	n/a	n/a
49	MAZ	chr2:190538941-190539773	GM12878	blood:	n/a	n/a
50	POLR2A	chr2:190538443-190539773	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:190538834..190541562-chr2:190626367..190628350,2	MCF-7	breast:
2	chr2:190525525..190526412-chr2:190538733..190539795,4	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-OSGEPL1-2	chr2:190538557-190539617	NONHSAT076058

Variant related genes	Relation type
ANKAR	TF binding region
ENSG00000253559	Chromatin interaction
ENSG00000128694	Chromatin interaction
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10197551	0.89[AFR][1000 genomes]
rs10197577	0.89[AFR][1000 genomes]
rs10497706	0.92[AFR][1000 genomes]
rs13390239	0.91[AFR][1000 genomes]
rs13400261	0.84[AFR][1000 genomes]
rs13404356	0.92[AFR][1000 genomes]
rs13411095	0.87[AFR][1000 genomes]
rs13416709	0.92[AFR][1000 genomes]
rs13418043	0.91[AFR][1000 genomes]
rs13418158	0.89[AFR][1000 genomes]
rs13418434	0.92[AFR][1000 genomes]
rs13429804	0.92[AFR][1000 genomes]
rs16831975	0.89[AFR][1000 genomes]
rs2118453	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs5742923	0.88[AFR][1000 genomes]
rs5742932	0.81[AFR][1000 genomes]
rs5742935	0.83[AFR][1000 genomes]
rs5742944	0.88[AFR][1000 genomes]
rs5742979	0.81[AFR][1000 genomes]
rs57785091	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6746951	0.88[AFR][1000 genomes]
rs6760126	0.87[AFR][1000 genomes]
rs73048418	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048432	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048437	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73048445	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73049960	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73050376	0.92[AFR][1000 genomes]
rs7560735	0.87[AFR][1000 genomes]
rs7577159	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190527400-190539000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:190527600-190539200	Weak transcription	Small Intestine	intestine
3	chr2:190528200-190541600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:190528600-190539600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:190530000-190542800	Strong transcription	Dnd41	blood
6	chr2:190532600-190539000	Weak transcription	Hela-S3	cervix
7	chr2:190533400-190539000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr2:190534000-190550200	Weak transcription	K562	blood
9	chr2:190536600-190539200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr2:190537400-190539000	Weak transcription	Ovary	ovary
11	chr2:190537600-190539000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr2:190538200-190539200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
13	chr2:190538400-190539000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr2:190538400-190539000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr2:190538400-190539000	Flanking Active TSS	Fetal Heart	heart
16	chr2:190538400-190539000	Flanking Active TSS	Osteobl	bone
17	chr2:190538400-190539200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:190538400-190539200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr2:190538400-190539200	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr2:190538400-190540000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr2:190538600-190539000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr2:190538600-190539000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr2:190538600-190539000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:190538600-190539000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr2:190538600-190539000	Flanking Active TSS	Primary B cells from cord blood	blood
26	chr2:190538600-190539000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
27	chr2:190538600-190539000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
28	chr2:190538600-190539000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr2:190538600-190539000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr2:190538600-190539000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr2:190538600-190539000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
32	chr2:190538600-190539000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr2:190538600-190539000	Flanking Active TSS	Brain Anterior Caudate	brain
34	chr2:190538600-190539000	Flanking Active TSS	Brain Cingulate Gyrus	brain
35	chr2:190538600-190539000	Flanking Active TSS	Brain Hippocampus Middle	brain
36	chr2:190538600-190539000	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
37	chr2:190538600-190539000	Flanking Active TSS	Brain Substantia Nigra	brain
38	chr2:190538600-190539000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr2:190538600-190539000	Flanking Active TSS	Fetal Brain Female	brain
40	chr2:190538600-190539000	Enhancers	Gastric	stomach
41	chr2:190538600-190539000	Enhancers	Placenta Amnion	Placenta Amnion
42	chr2:190538600-190539000	Flanking Active TSS	Rectal Smooth Muscle	rectum
43	chr2:190538600-190539000	Flanking Active TSS	Right Ventricle	heart
44	chr2:190538600-190539000	Flanking Active TSS	NH-A	brain
45	chr2:190538600-190539000	Flanking Active TSS	NHLF	lung
46	chr2:190538600-190539200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:190538600-190539200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
48	chr2:190538600-190539200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr2:190538600-190539200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr2:190538600-190539200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin

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