Variant report

Variant	rs11150586
Chromosome Location	chr16:30420851-30420852
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:22)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:22 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr16:30378764..30380971-chr16:30419142..30421108,2	K562	blood:
2	chr16:30420410..30423288-chr16:30429458..30434013,4	K562	blood:
3	chr16:30376934..30383374-chr16:30417165..30421108,8	K562	blood:
4	chr16:30387975..30389549-chr16:30419532..30421790,2	K562	blood:
5	chr16:30418204..30421021-chr16:30620059..30622629,3	MCF-7	breast:
6	chr16:30418404..30421860-chr16:30439556..30443342,4	K562	blood:
7	chr16:30411797..30412453-chr16:30420529..30421464,2	MCF-7	breast:
8	chr16:30363920..30364479-chr16:30420652..30421386,2	MCF-7	breast:
9	chr16:30366631..30368676-chr16:30418622..30421183,2	K562	blood:
10	chr16:30391959..30395001-chr16:30419499..30421472,4	K562	blood:
11	chr16:30420327..30422789-chr16:30456315..30458566,2	K562	blood:
12	chr16:30364739..30368463-chr16:30416926..30421783,8	MCF-7	breast:
13	chr16:30406155..30407445-chr16:30420427..30421180,3	K562	blood:
14	chr16:30381047..30382600-chr16:30420440..30421393,4	K562	blood:
15	chr16:30358199..30360201-chr16:30419831..30422515,2	MCF-7	breast:
16	chr16:30419670..30421306-chr16:30667705..30670395,2	K562	blood:
17	chr16:30420686..30421384-chr16:30639848..30640409,3	K562	blood:
18	chr16:30389715..30395001-chr16:30417296..30421020,7	K562	blood:
19	chr16:30406734..30407611-chr16:30420360..30421316,3	MCF-7	breast:
20	chr16:30387323..30391526-chr16:30418280..30422943,8	MCF-7	breast:
21	chr16:30420487..30421113-chr16:30609630..30610461,2	K562	blood:
22	chr16:30420772..30421274-chr16:30608906..30609785,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180209	Chromatin interaction
ENSG00000169217	Chromatin interaction
ENSG00000169221	Chromatin interaction
ENSG00000180096	Chromatin interaction
ENSG00000179958	Chromatin interaction
ENSG00000156860	Chromatin interaction
ENSG00000199787	Chromatin interaction
ENSG00000180035	Chromatin interaction
ENSG00000179918	Chromatin interaction
ENSG00000260219	Chromatin interaction
ENSG00000156853	Chromatin interaction
ENSG00000270466	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11640950	0.82[ASN][1000 genomes]
rs11646130	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs11862806	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs11863150	0.88[CEU][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs12446288	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs12921440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13333093	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35480350	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs35598865	1.00[JPT][hapmap]
rs3574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4340343	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4465620	0.88[CEU][hapmap];0.82[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.82[ASN][1000 genomes]
rs4787642	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4787643	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4788409	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap]
rs4788413	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs4788414	0.84[EUR][1000 genomes]
rs6565182	0.88[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs6565183	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs7203359	1.00[CHB][hapmap];0.92[GIH][hapmap];0.88[JPT][hapmap];0.84[TSI][hapmap]
rs8045252	0.95[ASN][1000 genomes]
rs8045570	0.95[ASN][1000 genomes]
rs8046445	0.92[CEU][hapmap];1.00[CHB][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap]
rs8049108	0.88[CEU][hapmap];1.00[CHB][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap]
rs8050812	1.00[JPT][hapmap]
rs8051096	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8060853	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs9888967	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065915	chr16:29967090-30486120	Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
2	nsv542897	chr16:29967090-30486120	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	229 gene(s)	inside rSNPs	diseases
3	nsv1056897	chr16:30363683-30457504	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	88 gene(s)	inside rSNPs	diseases
4	nsv905724	chr16:30368591-30438930	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	61 gene(s)	inside rSNPs	diseases
5	nsv532531	chr16:30370550-30581820	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
6	nsv827612	chr16:30371538-30429862	Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	59 gene(s)	inside rSNPs	diseases
7	nsv905725	chr16:30376959-30420851	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
8	nsv962197	chr16:30390489-30425618	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11150586	TBX6	cis	parietal	SCAN
rs11150586	MAPK3	cis	parietal	SCAN
rs11150586	IMAA///LOC440345///LOC440354///LOC595101///	N/A	lymphoblastoid	RTeQTL
rs11150586	BOLA2///LOC440354///LOC595101	N/A	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:30419200-30421200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
2	chr16:30419200-30421200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr16:30419200-30421200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr16:30419200-30421200	Enhancers	Placenta	Placenta
5	chr16:30419200-30421400	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr16:30419200-30422000	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr16:30419200-30428800	Weak transcription	Small Intestine	intestine
8	chr16:30419400-30421000	Flanking Active TSS	Dnd41	blood
9	chr16:30419400-30421400	Enhancers	Primary B cells from peripheral blood	blood
10	chr16:30419400-30421600	Enhancers	Primary T cells fromperipheralblood	blood
11	chr16:30419600-30421200	Enhancers	Primary hematopoietic stem cells	blood
12	chr16:30419600-30421200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:30419600-30421200	Enhancers	Ovary	ovary
14	chr16:30419600-30421200	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr16:30419600-30421400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr16:30419600-30421400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
17	chr16:30419600-30421400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
18	chr16:30419600-30421400	Enhancers	Primary T killer memory cells from peripheral blood	blood
19	chr16:30419600-30421400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr16:30419600-30421400	Enhancers	Fetal Lung	lung
21	chr16:30419600-30422000	Enhancers	Stomach Mucosa	stomach
22	chr16:30419600-30422200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr16:30419600-30422200	Genic enhancers	Fetal Stomach	stomach
24	chr16:30419600-30422600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr16:30419600-30423000	Weak transcription	Aorta	Aorta
26	chr16:30419600-30428600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr16:30419800-30421000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr16:30419800-30421000	Enhancers	Primary T helper cells fromperipheralblood	blood
29	chr16:30419800-30421000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr16:30419800-30421000	Enhancers	HMEC	breast
31	chr16:30419800-30421200	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr16:30419800-30421200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr16:30419800-30421200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr16:30419800-30421200	Enhancers	Fetal Brain Male	brain
35	chr16:30419800-30421200	Genic enhancers	Fetal Muscle Trunk	muscle
36	chr16:30419800-30421400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr16:30419800-30421400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr16:30419800-30421400	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr16:30419800-30421400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr16:30419800-30421400	Enhancers	Brain Substantia Nigra	brain
41	chr16:30419800-30421400	Enhancers	Pancreas	Pancrea
42	chr16:30419800-30421400	Enhancers	Rectal Mucosa Donor 29	rectum
43	chr16:30419800-30421400	Genic enhancers	K562	blood
44	chr16:30419800-30422200	Enhancers	HUVEC	blood vessel
45	chr16:30419800-30422800	Genic enhancers	Fetal Muscle Leg	muscle
46	chr16:30419800-30423000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr16:30419800-30423000	Weak transcription	Lung	lung
48	chr16:30419800-30423000	Weak transcription	Sigmoid Colon	Sigmoid Colon
49	chr16:30419800-30425200	Weak transcription	Psoas Muscle	Psoas
50	chr16:30419800-30425200	Weak transcription	Right Atrium	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links