Variant report

Variant	rs11609491
Chromosome Location	chr12:104899352-104899353
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:104889078..104893153-chr12:104897198..104902053,5	K562	blood:
2	chr12:104892344..104895135-chr12:104897977..104900926,3	MCF-7	breast:
3	chr12:104897397..104899517-chr12:104972120..104975034,2	K562	blood:
4	chr12:104898659..104900807-chr12:104906286..104908978,3	K562	blood:
5	chr12:104882770..104885599-chr12:104898967..104901298,2	K562	blood:
6	chr12:104897087..104900788-chr12:104905207..104908076,3	MCF-7	breast:
7	chr12:104899181..104901734-chr12:104930308..104932411,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000258111	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11608669	0.88[CEU][hapmap];0.85[CHB][hapmap];0.90[CHD][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17035663	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1882494	0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2141855	1.00[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141856	0.84[CHB][hapmap];0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4536299	0.86[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55778791	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56020814	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56138293	0.89[ASN][1000 genomes]
rs57525859	0.89[ASN][1000 genomes]
rs60351248	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970489	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7972097	0.82[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7972201	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832502	chr12:104833729-104908288	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv832504	chr12:104853331-105028245	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11609491	SCYL2	cis	parietal	SCAN
rs11609491	GOLGA2B	cis	cerebellum	SCAN

Chromatin state (count:83 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:104869200-104899600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:104875400-104904200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr12:104882600-104900600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:104887200-104903000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr12:104887600-104899400	Enhancers	Fetal Thymus	thymus
6	chr12:104888000-104900200	Weak transcription	Brain Substantia Nigra	brain
7	chr12:104890000-104903800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr12:104892600-104900200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr12:104892600-104900800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr12:104893000-104904400	Genic enhancers	Dnd41	blood
11	chr12:104893800-104900200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:104894400-104900200	Weak transcription	Fetal Lung	lung
13	chr12:104894400-104900400	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr12:104894400-104903800	Weak transcription	Rectal Smooth Muscle	rectum
15	chr12:104894800-104899400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:104894800-104900000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr12:104894800-104913000	Weak transcription	Rectal Mucosa Donor 29	rectum
18	chr12:104895000-104900000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr12:104895000-104900200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
20	chr12:104895600-104901200	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr12:104895600-104901400	Weak transcription	Primary T cells from cord blood	blood
22	chr12:104895600-104904000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr12:104895800-104899800	Weak transcription	Pancreas	Pancrea
24	chr12:104895800-104900200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr12:104896000-104900000	Weak transcription	Small Intestine	intestine
26	chr12:104896200-104899600	Weak transcription	Fetal Brain Female	brain
27	chr12:104896400-104900200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr12:104897000-104899400	Genic enhancers	Cortex derived primary cultured neurospheres	brain
29	chr12:104897000-104900600	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr12:104897000-104901600	Enhancers	ES-I3 Cell Line	embryonic stem cell
31	chr12:104897200-104901200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:104897400-104899600	Enhancers	Primary B cells from cord blood	blood
33	chr12:104897400-104905600	Enhancers	Primary B cells from peripheral blood	blood
34	chr12:104897600-104901800	Enhancers	Fetal Heart	heart
35	chr12:104897600-104903600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr12:104897600-104903800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr12:104897600-104907800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:104897800-104899400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr12:104897800-104900400	Enhancers	Duodenum Mucosa	Duodenum
40	chr12:104897800-104901600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr12:104898000-104899800	Enhancers	Aorta	Aorta
42	chr12:104898000-104901000	Enhancers	Gastric	stomach
43	chr12:104898000-104901800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:104898000-104903200	Weak transcription	Monocytes-CD14+_RO01746	blood
45	chr12:104898200-104899800	Enhancers	HSMMtube	muscle
46	chr12:104898200-104900000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
47	chr12:104898200-104900200	Weak transcription	Right Ventricle	heart
48	chr12:104898200-104900800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr12:104898200-104901400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr12:104898400-104899400	Enhancers	K562	blood

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