Variant report

Variant	rs56229595
Chromosome Location	chr2:11698133-11698134
allele	A/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	GATA3	chr2:11698032-11698188	SH-SY5Y	brain:	n/a	n/a
2	POLR2A	chr2:11697332-11700490	MCF-7	breast:	n/a	n/a
3	MXI1	chr2:11696692-11699565	SK-N-SH	brain:	n/a	n/a
4	E2F4	chr2:11698019-11698299	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11272919..11274870-chr2:11698095..11699910,2	K562	blood:
2	chr2:11260458..11262183-chr2:11697279..11699552,3	MCF-7	breast:

Variant related genes	Relation type
RNU2-13P	TF binding region
ENSG00000145063	Chromatin interaction
ENSG00000150873	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs2358038	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55665782	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55721526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55728517	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55816844	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55927874	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55995663	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56018731	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56198642	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56237365	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56700845	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58188623	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58357593	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58573299	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58849374	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58921396	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs58950938	0.97[AFR][1000 genomes]
rs61222790	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61386285	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6432217	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73915418	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915421	0.97[AFR][1000 genomes]
rs73915423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915426	0.97[AFR][1000 genomes]
rs73915427	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915428	0.97[AFR][1000 genomes]
rs73915429	0.97[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010506	chr2:11430965-12057286	Enhancers Strong transcription Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
2	nsv535585	chr2:11430965-12057286	Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
3	nsv873663	chr2:11664349-11783775	Genic enhancers Weak transcription ZNF genes & repeats Strong transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
4	esv1814335	chr2:11689048-11718858	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:11678400-11757000	Weak transcription	Right Ventricle	heart
2	chr2:11690000-11711000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr2:11691400-11699800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr2:11694200-11698400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:11694200-11698400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr2:11694600-11698200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr2:11694800-11699200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr2:11694800-11699600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:11694800-11755200	Weak transcription	Gastric	stomach
10	chr2:11696000-11699800	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr2:11696200-11700400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr2:11696400-11700200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
13	chr2:11696800-11698200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr2:11697000-11698600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr2:11697000-11702200	Weak transcription	Pancreas	Pancrea
16	chr2:11697000-11706800	Weak transcription	Brain Cingulate Gyrus	brain
17	chr2:11697000-11710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
19	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
20	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain
21	chr2:11697400-11698200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
22	chr2:11697400-11699000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr2:11697600-11698600	Enhancers	H1 Cell Line	embryonic stem cell
24	chr2:11697600-11699800	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr2:11697600-11699800	Enhancers	Fetal Heart	heart
26	chr2:11697600-11700200	Enhancers	Left Ventricle	heart
27	chr2:11697600-11700400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr2:11697600-11700600	Transcr. at gene 5' and 3'	Ovary	ovary
29	chr2:11697800-11698600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:11697800-11698600	Enhancers	iPS-20b Cell Line	embryonic stem cell
31	chr2:11697800-11698800	Enhancers	iPS-18 Cell Line	embryonic stem cell
32	chr2:11697800-11699000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
33	chr2:11697800-11706800	Weak transcription	Brain Substantia Nigra	brain
34	chr2:11698000-11699000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr2:11698000-11699000	Genic enhancers	HepG2	liver
36	chr2:11698000-11699200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr2:11698000-11699200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr2:11698000-11699800	Enhancers	Fetal Adrenal Gland	Adrenal Gland

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links