Variant report

Variant	rs12220818
Chromosome Location	chr10:6517476-6517477
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:6506742..6509620-chr10:6514468..6518206,3	K562	blood:
2	chr10:6505761..6513673-chr10:6513705..6518581,11	K562	blood:
3	chr10:6515689..6518540-chr10:6536895..6539799,2	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11258747	0.82[CHB][hapmap]
rs11258943	0.82[CHB][hapmap]
rs11259097	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[ASN][1000 genomes]
rs11259163	0.89[ASN][1000 genomes]
rs12218210	1.00[YRI][hapmap]
rs1537320	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs17152987	1.00[YRI][hapmap]
rs17372283	0.82[CHB][hapmap]
rs494800	1.00[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs584724	0.82[CHB][hapmap]
rs6602745	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042286	chr10:5795129-6578445	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	nsv1053440	chr10:6354798-6669469	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
3	nsv1047309	chr10:6495583-6714060	Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12220818	UCN3	cis	cerebellum	SCAN
rs12220818	PFKFB3	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:6496600-6539200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr10:6498400-6537000	Weak transcription	HUES48 Cell Line	embryonic stem cell
3	chr10:6498600-6518800	Weak transcription	Fetal Stomach	stomach
4	chr10:6499000-6527800	Weak transcription	Pancreas	Pancrea
5	chr10:6499200-6562000	Weak transcription	Brain Anterior Caudate	brain
6	chr10:6501600-6527200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr10:6501800-6557000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr10:6502200-6518800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr10:6503000-6533000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr10:6504400-6518200	Weak transcription	HUES64 Cell Line	embryonic stem cell
11	chr10:6504600-6524200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr10:6506200-6520400	Weak transcription	Fetal Muscle Leg	muscle
13	chr10:6509200-6541200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr10:6509800-6517600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr10:6509800-6533000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr10:6510000-6572000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr10:6513200-6517600	Weak transcription	Skeletal Muscle Male	skeletal muscle
18	chr10:6513400-6517600	Weak transcription	Skeletal Muscle Female	skeletal muscle
19	chr10:6514000-6540000	Weak transcription	Psoas Muscle	Psoas
20	chr10:6514400-6518200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr10:6515000-6518800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr10:6515400-6518200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr10:6515400-6520000	Enhancers	NHEK	skin
24	chr10:6516000-6517600	Enhancers	Fetal Kidney	kidney
25	chr10:6516000-6518200	Enhancers	Fetal Intestine Small	intestine
26	chr10:6516200-6518000	Enhancers	K562	blood
27	chr10:6516400-6517800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
28	chr10:6516400-6517800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
29	chr10:6516400-6517800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr10:6516400-6518000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr10:6516400-6518600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
32	chr10:6516400-6518600	Weak transcription	HMEC	breast
33	chr10:6516400-6518800	Enhancers	Primary hematopoietic stem cells short term culture	blood
34	chr10:6516400-6518800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr10:6516400-6535800	Weak transcription	Duodenum Mucosa	Duodenum
36	chr10:6516600-6517600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr10:6516600-6518200	Enhancers	Primary hematopoietic stem cells	blood
38	chr10:6516600-6518800	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr10:6516600-6523000	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr10:6516800-6518200	Genic enhancers	Thymus	Thymus
41	chr10:6516800-6519000	Genic enhancers	Primary T cells from cord blood	blood
42	chr10:6517000-6517600	Enhancers	Fetal Intestine Large	intestine
43	chr10:6517000-6518800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
44	chr10:6517000-6531800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr10:6517200-6517800	Enhancers	Brain Hippocampus Middle	brain
46	chr10:6517200-6518000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
47	chr10:6517200-6518200	Genic enhancers	Primary T helper cells fromperipheralblood	blood
48	chr10:6517200-6518800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr10:6517200-6557800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
50	chr10:6517400-6517600	Enhancers	Dnd41	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links