Variant report

Variant	rs11629613
Chromosome Location	chr15:55577303-55577304
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:55538847..55540639-chr15:55576116..55578035,2	MCF-7	breast:
2	chr15:55566058..55568743-chr15:55575298..55578143,3	K562	blood:
3	chr15:55576187..55578993-chr15:55609821..55611472,2	MCF-7	breast:
4	chr15:55563187..55564952-chr15:55575957..55578942,3	K562	blood:
5	chr15:55575274..55577450-chr15:55698113..55700653,2	K562	blood:

Variant related genes	Relation type
ENSG00000260916	Chromatin interaction
ENSG00000069974	Chromatin interaction
ENSG00000225973	Chromatin interaction
ENSG00000069943	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10851588	1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs11071174	0.91[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071176	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071180	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs11071181	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs11490399	0.81[ASN][1000 genomes]
rs11630409	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11632757	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs11634665	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11635532	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11636687	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11638111	0.85[ASN][1000 genomes]
rs11638732	0.94[ASN][1000 genomes]
rs11639418	0.95[CHB][hapmap];0.80[JPT][hapmap];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11639453	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857303	0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs12050587	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs12050662	0.81[ASN][1000 genomes]
rs12050663	0.81[ASN][1000 genomes]
rs12050885	0.91[CHB][hapmap];0.80[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12050905	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2290341	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs2290343	0.85[ASN][1000 genomes]
rs2290344	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2305424	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414409	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs28540063	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28657774	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28668016	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs28680176	0.81[ASN][1000 genomes]
rs28706887	0.90[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs28748576	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs34848296	0.83[ASN][1000 genomes]
rs3743203	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs4774760	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs4774764	0.81[ASN][1000 genomes]
rs4774766	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs55661134	0.84[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs55933611	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55957229	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56159619	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56257633	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs58701687	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs60338710	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60375490	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61387252	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61573749	0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs67230579	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs67603645	0.90[ASN][1000 genomes]
rs692062	0.81[CEU][hapmap]
rs7162777	0.87[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs7174876	0.86[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7183157	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs7183960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs72742273	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72742282	0.82[ASN][1000 genomes]
rs8024695	1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8034229	0.89[ASN][1000 genomes]
rs9920058	1.00[CHB][hapmap];0.95[JPT][hapmap];0.80[YRI][hapmap];0.82[ASN][1000 genomes]
rs9920522	1.00[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	nsv1040917	chr15:55562940-55943942	Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv531054	chr15:55571230-55914205	Strong transcription Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11629613	PIGB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:55542400-55581000	Weak transcription	Fetal Intestine Small	intestine
2	chr15:55553200-55581000	Weak transcription	Fetal Intestine Large	intestine
3	chr15:55567800-55580800	Weak transcription	Fetal Stomach	stomach
4	chr15:55569400-55578200	Weak transcription	Fetal Kidney	kidney
5	chr15:55570200-55580400	Weak transcription	Fetal Thymus	thymus
6	chr15:55570200-55581200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:55570600-55580800	Weak transcription	Rectal Mucosa Donor 29	rectum
8	chr15:55571200-55577800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
9	chr15:55572000-55580800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:55572200-55581000	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:55572400-55580800	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr15:55572600-55580000	Weak transcription	HepG2	liver
13	chr15:55572600-55581000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:55573200-55578200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr15:55573200-55579000	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr15:55573400-55577400	Genic enhancers	K562	blood
17	chr15:55573600-55579600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr15:55573800-55578400	Enhancers	Primary hematopoietic stem cells	blood
19	chr15:55574200-55581000	Weak transcription	Fetal Muscle Leg	muscle
20	chr15:55574400-55581400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr15:55574600-55577800	Weak transcription	Aorta	Aorta
22	chr15:55574800-55578600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr15:55574800-55581000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr15:55575000-55581000	Weak transcription	Esophagus	oesophagus
25	chr15:55575000-55581000	Weak transcription	Right Ventricle	heart
26	chr15:55575000-55581200	Weak transcription	Left Ventricle	heart
27	chr15:55575200-55577400	Strong transcription	Primary T cells from cord blood	blood
28	chr15:55575200-55578200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr15:55575200-55578800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr15:55575200-55579000	Enhancers	Primary T helper naive cells from peripheral blood	blood
31	chr15:55575200-55580800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
32	chr15:55575200-55580800	Weak transcription	Stomach Smooth Muscle	stomach
33	chr15:55575200-55581000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr15:55575200-55581000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
35	chr15:55575200-55581000	Weak transcription	Gastric	stomach
36	chr15:55575200-55581000	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr15:55575200-55581000	Weak transcription	NHEK	skin
38	chr15:55575400-55578200	Enhancers	Primary T killer memory cells from peripheral blood	blood
39	chr15:55575400-55578800	Enhancers	Primary T cells fromperipheralblood	blood
40	chr15:55575400-55579000	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
41	chr15:55575400-55580400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr15:55575400-55580800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr15:55575400-55581000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr15:55575400-55581000	Weak transcription	NHDF-Ad	bronchial
45	chr15:55575400-55581000	Weak transcription	NHLF	lung
46	chr15:55575400-55581000	Weak transcription	Osteobl	bone
47	chr15:55575400-55581200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:55575600-55578000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:55575600-55580400	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:55575600-55580800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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