Variant report

Variant	rs58950938
Chromosome Location	chr2:11700990-11700991
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	POLR2A	chr2:11700890-11701526	HepG2	liver:	n/a	n/a
2	POLR2A	chr2:11700853-11701509	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:11698164..11701125-chr2:11728905..11731713,2	K562	blood:
2	chr2:11699009..11701296-chr2:218182757..218185396,2	MCF-7	breast:

Variant related genes	Relation type
RNU2-13P	TF binding region

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10427206	1.00[EUR][1000 genomes]
rs10520085	1.00[EUR][1000 genomes]
rs16857583	1.00[EUR][1000 genomes]
rs2358038	0.95[AFR][1000 genomes]
rs55665782	0.95[AFR][1000 genomes]
rs55721526	0.97[AFR][1000 genomes]
rs55728517	0.95[AFR][1000 genomes]
rs55816844	0.92[AFR][1000 genomes]
rs55927874	0.95[AFR][1000 genomes]
rs55995663	0.97[AFR][1000 genomes]
rs56018731	0.95[AFR][1000 genomes]
rs56198642	0.97[AFR][1000 genomes]
rs56229595	0.97[AFR][1000 genomes]
rs56237365	0.95[AFR][1000 genomes]
rs56700845	0.92[AFR][1000 genomes]
rs56714132	1.00[EUR][1000 genomes]
rs56805168	1.00[EUR][1000 genomes]
rs57108153	1.00[EUR][1000 genomes]
rs57932839	1.00[EUR][1000 genomes]
rs58188623	0.92[AFR][1000 genomes]
rs58573299	0.92[AFR][1000 genomes]
rs58849374	0.87[AFR][1000 genomes]
rs58921396	0.95[AFR][1000 genomes]
rs59489734	1.00[EUR][1000 genomes]
rs59636084	1.00[EUR][1000 genomes]
rs59936690	1.00[EUR][1000 genomes]
rs60215345	1.00[EUR][1000 genomes]
rs61039324	1.00[EUR][1000 genomes]
rs61222790	0.92[AFR][1000 genomes]
rs61386285	0.92[AFR][1000 genomes]
rs73180151	1.00[EUR][1000 genomes]
rs73187491	1.00[EUR][1000 genomes]
rs73187494	1.00[EUR][1000 genomes]
rs73189350	1.00[EUR][1000 genomes]
rs73189353	1.00[EUR][1000 genomes]
rs73189354	1.00[EUR][1000 genomes]
rs73189377	1.00[EUR][1000 genomes]
rs73915418	0.92[AFR][1000 genomes]
rs73915421	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915423	0.97[AFR][1000 genomes]
rs73915425	1.00[EUR][1000 genomes]
rs73915426	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915427	0.95[AFR][1000 genomes]
rs73915428	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73915429	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs73915430	1.00[EUR][1000 genomes]
rs73915431	1.00[EUR][1000 genomes]
rs73915432	1.00[EUR][1000 genomes]
rs73915433	1.00[EUR][1000 genomes]
rs73915434	1.00[EUR][1000 genomes]
rs73915435	1.00[EUR][1000 genomes]
rs73915443	1.00[EUR][1000 genomes]
rs73917236	1.00[EUR][1000 genomes]
rs73917248	1.00[EUR][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:40 , 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	chr2:11694800-11755200	Weak transcription	Gastric	stomach
4	chr2:11697000-11702200	Weak transcription	Pancreas	Pancrea
5	chr2:11697000-11706800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:11697000-11710800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr2:11697000-11722600	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:11697000-11723000	Weak transcription	Brain Anterior Caudate	brain
9	chr2:11697000-11723200	Weak transcription	Brain Angular Gyrus	brain
10	chr2:11697800-11706800	Weak transcription	Brain Substantia Nigra	brain
11	chr2:11698600-11713200	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr2:11698600-11713400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr2:11698800-11703600	Weak transcription	Skeletal Muscle Female	skeletal muscle
14	chr2:11698800-11706200	Weak transcription	Fetal Muscle Leg	muscle
15	chr2:11698800-11713400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr2:11699000-11701000	Strong transcription	HepG2	liver
17	chr2:11699000-11714400	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr2:11699400-11706600	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr2:11699400-11706800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:11699800-11701800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr2:11699800-11702400	Weak transcription	Fetal Stomach	stomach
22	chr2:11699800-11703400	Weak transcription	Fetal Heart	heart
23	chr2:11699800-11708400	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr2:11699800-11713200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:11699800-11718400	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr2:11699800-11723000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr2:11700000-11702400	Weak transcription	Fetal Muscle Trunk	muscle
28	chr2:11700000-11767000	Weak transcription	Right Atrium	heart
29	chr2:11700200-11701800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr2:11700200-11712400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr2:11700200-11713800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr2:11700200-11723000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr2:11700400-11701800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:11700400-11702200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr2:11700400-11703000	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr2:11700400-11705200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
37	chr2:11700400-11706800	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr2:11700400-11713000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr2:11700400-11718400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr2:11700600-11709600	Genic enhancers	Ovary	ovary

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