Variant report

Variant	rs11857604
Chromosome Location	chr15:34493311-34493312
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:34493054..34495397-chr15:34496160..34499059,3	MCF-7	breast:
2	chr15:34479489..34481892-chr15:34492383..34494065,2	K562	blood:
3	chr15:34487048..34490897-chr15:34492238..34496487,4	K562	blood:
4	chr15:34491377..34494902-chr15:34500682..34503965,3	K562	blood:

Variant related genes	Relation type
ENSG00000134152	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs10152261	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11852315	0.82[ASN][1000 genomes]
rs11853345	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11853347	0.82[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11854298	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11856753	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11857608	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11858527	0.82[ASN][1000 genomes]
rs17236749	0.82[ASN][1000 genomes]
rs17554484	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17817770	0.82[ASN][1000 genomes]
rs2118159	0.82[ASN][1000 genomes]
rs2118160	0.82[ASN][1000 genomes]
rs28406544	0.82[ASN][1000 genomes]
rs3764236	0.82[ASN][1000 genomes]
rs3829483	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs41405647	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4486849	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4581678	0.82[ASN][1000 genomes]
rs55801303	0.82[ASN][1000 genomes]
rs6495624	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161944	0.82[ASN][1000 genomes]
rs7168139	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7176526	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7179249	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73382081	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73382086	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73384011	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8037674	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672345	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672434	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672496	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9672544	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9672784	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9806468	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035579	chr15:34363159-34501115	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11857604	C15orf29	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:34454200-34497800	Weak transcription	Osteobl	bone
2	chr15:34454600-34501200	Weak transcription	Colonic Mucosa	Colon
3	chr15:34454800-34501000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
4	chr15:34464600-34500400	Weak transcription	Hela-S3	cervix
5	chr15:34466400-34500400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr15:34467000-34500800	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr15:34467200-34500200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr15:34468000-34496400	Weak transcription	Fetal Lung	lung
9	chr15:34468000-34497800	Weak transcription	NHEK	skin
10	chr15:34468200-34498000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr15:34471000-34501000	Weak transcription	Aorta	Aorta
12	chr15:34471600-34500400	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:34473400-34500400	Weak transcription	HSMMtube	muscle
14	chr15:34475000-34500400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:34475600-34493600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr15:34475600-34495600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:34475600-34499800	Weak transcription	Ovary	ovary
18	chr15:34475600-34500000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr15:34475600-34500400	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:34475600-34500400	Weak transcription	Colon Smooth Muscle	Colon
21	chr15:34475600-34500400	Weak transcription	HUVEC	blood vessel
22	chr15:34476200-34499600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:34476200-34500000	Weak transcription	Fetal Brain Female	brain
24	chr15:34476400-34500800	Weak transcription	Rectal Mucosa Donor 31	rectum
25	chr15:34476800-34499800	Weak transcription	Primary T cells fromperipheralblood	blood
26	chr15:34477000-34499800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr15:34477200-34500000	Weak transcription	Liver	Liver
28	chr15:34477600-34501000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr15:34477600-34501200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
30	chr15:34478000-34500200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:34478600-34496400	Weak transcription	HSMM	muscle
32	chr15:34478800-34500000	Weak transcription	Fetal Intestine Large	intestine
33	chr15:34478800-34500400	Weak transcription	Thymus	Thymus
34	chr15:34478800-34500800	Weak transcription	Primary hematopoietic stem cells	blood
35	chr15:34479000-34498200	Weak transcription	NH-A	brain
36	chr15:34479200-34500000	Weak transcription	Esophagus	oesophagus
37	chr15:34479200-34500800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr15:34479200-34501000	Weak transcription	Gastric	stomach
39	chr15:34479400-34500800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:34479400-34501000	Weak transcription	Left Ventricle	heart
41	chr15:34479400-34501600	Weak transcription	Lung	lung
42	chr15:34479600-34500800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr15:34479600-34501800	Weak transcription	Spleen	Spleen
44	chr15:34480000-34500000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr15:34480000-34500800	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:34480400-34500400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:34480600-34498600	Weak transcription	Fetal Intestine Small	intestine
48	chr15:34481000-34500400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:34481000-34500800	Weak transcription	Brain Cingulate Gyrus	brain
50	chr15:34481600-34498200	Weak transcription	Placenta	Placenta

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