Variant report

Variant	rs11630409
Chromosome Location	chr15:55561887-55561888
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:55531824..55534011-chr15:55559781..55562269,2	K562	blood:
2	chr15:55529177..55531366-chr15:55559639..55562184,2	K562	blood:

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11071174	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071176	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11629613	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11634665	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11635532	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636687	0.85[ASN][1000 genomes]
rs11638732	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11639418	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11639453	0.87[ASN][1000 genomes]
rs11639469	0.81[ASN][1000 genomes]
rs11857303	0.86[ASN][1000 genomes]
rs12050885	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12050905	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290344	0.81[EUR][1000 genomes]
rs2305424	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28540063	0.87[ASN][1000 genomes]
rs28668016	0.83[ASN][1000 genomes]
rs34848296	0.81[ASN][1000 genomes]
rs4261468	0.81[ASN][1000 genomes]
rs4774760	0.87[ASN][1000 genomes]
rs55661134	0.83[ASN][1000 genomes]
rs55933611	0.83[ASN][1000 genomes]
rs55957229	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56042059	0.81[ASN][1000 genomes]
rs56159619	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56257633	0.83[ASN][1000 genomes]
rs58701687	0.87[ASN][1000 genomes]
rs60338710	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60375490	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61387252	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61573749	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67230579	0.85[ASN][1000 genomes]
rs67603645	0.88[ASN][1000 genomes]
rs7162777	0.87[ASN][1000 genomes]
rs7183157	0.80[ASN][1000 genomes]
rs72742273	0.87[ASN][1000 genomes]
rs7496857	0.81[ASN][1000 genomes]
rs8034229	0.94[ASN][1000 genomes]
rs9920058	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043176	chr15:55010228-55563000	Genic enhancers Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv1042741	chr15:55068022-55622497	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv917323	chr15:55290499-56041334	Genic enhancers Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
4	nsv1043789	chr15:55400872-56092454	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv1036924	chr15:55527874-55616480	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv1051046	chr15:55529291-55821973	Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
7	nsv569522	chr15:55532211-55611126	Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Weak transcription 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	14 gene(s)	inside rSNPs	diseases
8	nsv904241	chr15:55534342-55611126	Weak transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
9	nsv1036173	chr15:55547689-55812194	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
10	nsv542391	chr15:55547689-55812194	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
11	nsv904242	chr15:55550755-55611126	Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv569523	chr15:55555602-55836704	Weak transcription Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
13	nsv569524	chr15:55558624-55612511	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11630409	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55490000-55562800	Weak transcription	Ovary	ovary
2	chr15:55520800-55574800	Weak transcription	Stomach Smooth Muscle	stomach
3	chr15:55542400-55581000	Weak transcription	Fetal Intestine Small	intestine
4	chr15:55547800-55571400	Weak transcription	Aorta	Aorta
5	chr15:55548600-55574800	Weak transcription	Left Ventricle	heart
6	chr15:55549200-55571600	Weak transcription	HMEC	breast
7	chr15:55550000-55571400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr15:55553200-55581000	Weak transcription	Fetal Intestine Large	intestine
9	chr15:55559600-55563200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:55559800-55562800	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:55559800-55569400	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr15:55559800-55571200	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr15:55560000-55562600	Weak transcription	Colon Smooth Muscle	Colon
14	chr15:55560000-55566200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr15:55560200-55563200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr15:55560200-55567400	Weak transcription	Gastric	stomach
17	chr15:55560200-55569800	Weak transcription	Hela-S3	cervix
18	chr15:55560200-55571200	Weak transcription	NHDF-Ad	bronchial
19	chr15:55560200-55574800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr15:55560200-55575400	Weak transcription	Thymus	Thymus
21	chr15:55560400-55562400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:55560400-55564600	Enhancers	Primary T cells fromperipheralblood	blood
23	chr15:55560400-55565000	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr15:55560400-55568600	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr15:55560400-55571800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr15:55560600-55562200	Enhancers	Primary T helper cells PMA-I stimulated	--
27	chr15:55560600-55562400	Weak transcription	Cortex derived primary cultured neurospheres	brain
28	chr15:55560600-55562800	Genic enhancers	Primary neutrophils fromperipheralblood	blood
29	chr15:55560600-55563400	Genic enhancers	Monocytes-CD14+_RO01746	blood
30	chr15:55560600-55565200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
31	chr15:55560600-55568200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr15:55560600-55569000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr15:55560600-55569600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr15:55560600-55569600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr15:55560800-55562600	Weak transcription	NH-A	brain
36	chr15:55560800-55563600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr15:55560800-55565200	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr15:55560800-55567600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:55560800-55569400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:55561000-55562800	Weak transcription	Stomach Mucosa	stomach
41	chr15:55561000-55563600	Genic enhancers	Primary monocytes fromperipheralblood	blood
42	chr15:55561000-55563800	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:55561000-55567600	Weak transcription	Primary B cells from peripheral blood	blood
44	chr15:55561200-55562000	Strong transcription	Fetal Stomach	stomach
45	chr15:55561200-55562400	Weak transcription	Primary T helper cells fromperipheralblood	blood
46	chr15:55561200-55568600	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:55561400-55562400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
48	chr15:55561400-55565000	Weak transcription	K562	blood
49	chr15:55561400-55567400	Weak transcription	Primary B cells from cord blood	blood
50	chr15:55561400-55571400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links