Variant report

Variant	rs772558
Chromosome Location	chr12:63304629-63304630
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:63302887..63305750-chr12:63328233..63330331,2	K562	blood:
2	chr12:63298026..63301472-chr12:63301744..63306217,4	K562	blood:
3	chr12:63303143..63306102-chr12:63308178..63311320,4	K562	blood:
4	chr12:63303196..63305906-chr12:63305926..63307721,2	K562	blood:

Variant related genes	Relation type
ENSG00000111110	Chromatin interaction
ENSG00000252660	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs699576	0.91[JPT][hapmap]
rs699578	0.81[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs699581	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs771987	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs771989	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs772562	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs772564	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs772570	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs772571	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs814009	0.95[CEU][hapmap];0.81[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][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	esv3415227	chr12:63228121-63591615	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv899161	chr12:63275017-63311148	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	nsv899162	chr12:63279750-63334242	Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	9 gene(s)	inside rSNPs	diseases
4	nsv899163	chr12:63288343-63325988	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	4 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	chr12:63287400-63309000	Weak transcription	Pancreas	Pancrea
2	chr12:63287800-63316400	Weak transcription	Fetal Intestine Small	intestine
3	chr12:63289600-63306600	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr12:63292800-63311600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:63296400-63307200	Weak transcription	Left Ventricle	heart
6	chr12:63297400-63309600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr12:63300800-63304800	Enhancers	K562	blood
8	chr12:63301200-63313400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:63301600-63306200	Weak transcription	Brain Substantia Nigra	brain
10	chr12:63301600-63306400	Enhancers	Primary hematopoietic stem cells	blood
11	chr12:63301600-63307800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:63301800-63306800	Weak transcription	Brain Angular Gyrus	brain
13	chr12:63301800-63307200	Weak transcription	Brain Anterior Caudate	brain
14	chr12:63301800-63307400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
15	chr12:63301800-63307800	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:63301800-63309000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr12:63301800-63313600	Weak transcription	Aorta	Aorta
18	chr12:63303000-63306200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr12:63303200-63304800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr12:63303200-63305000	Enhancers	HUES64 Cell Line	embryonic stem cell
21	chr12:63303200-63305600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
22	chr12:63303400-63305400	Enhancers	Pancreatic Islets	Pancreatic Islet
23	chr12:63303400-63313000	Weak transcription	Ovary	ovary
24	chr12:63303800-63304800	Strong transcription	HepG2	liver
25	chr12:63303800-63305000	Enhancers	Fetal Intestine Large	intestine
26	chr12:63303800-63307200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr12:63304000-63305000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr12:63304000-63305000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr12:63304000-63305200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr12:63304000-63305200	Weak transcription	Gastric	stomach
31	chr12:63304000-63306600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr12:63304000-63307800	Weak transcription	Brain Cingulate Gyrus	brain
33	chr12:63304000-63308200	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr12:63304400-63305000	Enhancers	Stomach Mucosa	stomach
35	chr12:63304400-63305400	Enhancers	HUES6 Cell Line	embryonic stem cell
36	chr12:63304600-63305000	Enhancers	HUES48 Cell Line	embryonic stem cell
37	chr12:63304600-63305000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr12:63304600-63307000	Weak transcription	H9 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links