Variant report

Variant	rs10863650
Chromosome Location	chr1:221897213-221897214
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:221895265..221897996-chr1:222013655..222015689,2	K562	blood:
2	chr1:221896601..221898804-chr1:221901497..221903460,2	K562	blood:
3	chr1:221891993..221895094-chr1:221895705..221898533,3	K562	blood:
4	chr1:221887650..221891571-chr1:221892438..221898117,9	K562	blood:
5	chr1:221895037..221902178-chr1:221912556..221917116,9	K562	blood:
6	chr1:221897172..221898775-chr1:222217988..222220740,2	K562	blood:

Variant related genes	Relation type
ENSG00000143507	Chromatin interaction
ENSG00000227925	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10779455	1.00[ASN][1000 genomes]
rs11118830	1.00[ASN][1000 genomes]
rs11118832	1.00[ASN][1000 genomes]
rs11118849	1.00[ASN][1000 genomes]
rs11118851	1.00[ASN][1000 genomes]
rs11576121	1.00[ASN][1000 genomes]
rs12058360	1.00[ASN][1000 genomes]
rs12129426	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134197	0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12134869	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4275462	0.92[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.90[EUR][1000 genomes]
rs58058349	1.00[ASN][1000 genomes]
rs58969712	1.00[ASN][1000 genomes]
rs60950693	1.00[ASN][1000 genomes]
rs6679673	1.00[ASN][1000 genomes]
rs6689267	0.92[CEU][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6693577	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67225019	1.00[ASN][1000 genomes]
rs72736551	1.00[ASN][1000 genomes]
rs72736552	1.00[ASN][1000 genomes]
rs72736557	1.00[ASN][1000 genomes]
rs72736561	1.00[ASN][1000 genomes]
rs72736562	1.00[ASN][1000 genomes]
rs72736563	1.00[ASN][1000 genomes]
rs72736571	1.00[ASN][1000 genomes]
rs7340042	1.00[ASN][1000 genomes]
rs7534227	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7549374	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv469786	chr1:221855871-222040335	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv482867	chr1:221855871-222040335	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1002463	chr1:221863355-222095773	Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
4	nsv535302	chr1:221863355-222095773	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv1007092	chr1:221883491-221958279	Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	nsv535303	chr1:221883491-221958279	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10863650	TGFB2	cis	cerebellum	SCAN

Chromatin state (count:88 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:221879600-221902400	Enhancers	Brain Substantia Nigra	brain
2	chr1:221882800-221899000	Genic enhancers	HSMM	muscle
3	chr1:221887200-221899000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr1:221887800-221898400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
5	chr1:221888000-221899000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
6	chr1:221888000-221903000	Enhancers	Brain Hippocampus Middle	brain
7	chr1:221888800-221898600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr1:221889400-221899600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:221889800-221899000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr1:221890400-221898400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr1:221890800-221906400	Weak transcription	Right Ventricle	heart
12	chr1:221890800-221910200	Weak transcription	Lung	lung
13	chr1:221891800-221911000	Weak transcription	Gastric	stomach
14	chr1:221891800-221913000	Weak transcription	Fetal Intestine Large	intestine
15	chr1:221892200-221898200	Enhancers	HSMMtube	muscle
16	chr1:221892400-221901400	Weak transcription	Small Intestine	intestine
17	chr1:221892600-221898000	Weak transcription	Stomach Mucosa	stomach
18	chr1:221892800-221897400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr1:221892800-221899000	Weak transcription	Thymus	Thymus
20	chr1:221893000-221913600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr1:221893200-221898000	Weak transcription	Rectal Mucosa Donor 31	rectum
22	chr1:221893200-221899400	Genic enhancers	Liver	Liver
23	chr1:221894600-221898000	Enhancers	Skeletal Muscle Female	skeletal muscle
24	chr1:221894600-221899800	Enhancers	Brain Angular Gyrus	brain
25	chr1:221894800-221897400	Enhancers	Brain Inferior Temporal Lobe	brain
26	chr1:221894800-221897600	Enhancers	K562	blood
27	chr1:221894800-221898600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
28	chr1:221894800-221898800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr1:221895000-221898000	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr1:221895000-221898400	Enhancers	Psoas Muscle	Psoas
31	chr1:221895200-221897600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
32	chr1:221895200-221900800	Enhancers	Brain Cingulate Gyrus	brain
33	chr1:221895400-221897600	Genic enhancers	Muscle Satellite Cultured Cells	--
34	chr1:221895400-221897600	Transcr. at gene 5' and 3'	GM12878-XiMat	blood
35	chr1:221895400-221901400	Enhancers	Brain Anterior Caudate	brain
36	chr1:221895400-221901800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr1:221895600-221897600	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
38	chr1:221896000-221897600	ZNF genes & repeats	HMEC	breast
39	chr1:221896000-221897800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
40	chr1:221896000-221898000	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr1:221896000-221899400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr1:221896000-221899800	Enhancers	NH-A	brain
43	chr1:221896000-221900200	Enhancers	Hela-S3	cervix
44	chr1:221896200-221897600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr1:221896200-221898200	ZNF genes & repeats	Primary hematopoietic stem cells	blood
46	chr1:221896200-221898800	Weak transcription	Right Atrium	heart
47	chr1:221896400-221897400	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
48	chr1:221896400-221897400	ZNF genes & repeats	HepG2	liver
49	chr1:221896400-221897600	ZNF genes & repeats	Fetal Thymus	thymus
50	chr1:221896400-221897600	ZNF genes & repeats	NHEK	skin

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