Variant report

Variant	rs4942863
Chromosome Location	chr13:50314408-50314409
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	chr13:50312252..50315193-chr13:50321361..50323993,2	MCF-7	breast:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1009333	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs10492591	0.93[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1127021	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1198315	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1198319	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1198320	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1198322	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1198324	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1201716	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1211304	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1407440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1407441	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1547623	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1570353	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1581745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2025263	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2146143	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs2181185	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2407804	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2897770	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3851162	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61961491	0.86[AMR][1000 genomes]
rs6561552	0.92[CEU][hapmap];0.90[YRI][hapmap]
rs6561560	0.92[CEU][hapmap]
rs7330392	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7983303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7984061	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9316474	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9526591	0.93[EUR][1000 genomes]
rs9526593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535305	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9535307	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535310	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9535316	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9535330	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs9535340	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9535341	0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9562927	0.95[YRI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4942863	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs4942863	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:113 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266200-50316000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
3	chr13:50273200-50326000	Weak transcription	Aorta	Aorta
4	chr13:50273200-50333800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr13:50277000-50318400	Weak transcription	Hela-S3	cervix
6	chr13:50290000-50324000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
7	chr13:50290000-50334000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr13:50290200-50316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr13:50293200-50326000	Weak transcription	Fetal Brain Male	brain
10	chr13:50294200-50315000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr13:50294200-50324000	Weak transcription	Rectal Smooth Muscle	rectum
12	chr13:50294400-50333000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
13	chr13:50296200-50330400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr13:50296400-50320200	Weak transcription	Spleen	Spleen
15	chr13:50296600-50330400	Weak transcription	Small Intestine	intestine
16	chr13:50296600-50338600	Weak transcription	Ovary	ovary
17	chr13:50296800-50315000	Weak transcription	HMEC	breast
18	chr13:50297000-50322400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr13:50298000-50327600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr13:50299200-50327600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr13:50299400-50319400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:50300800-50321800	Weak transcription	Brain Anterior Caudate	brain
24	chr13:50301000-50319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr13:50301200-50316000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr13:50301200-50323600	Weak transcription	Colon Smooth Muscle	Colon
27	chr13:50301200-50327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:50302800-50333800	Weak transcription	Thymus	Thymus
29	chr13:50303200-50319400	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr13:50303200-50334000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr13:50304400-50316000	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr13:50304400-50321400	Weak transcription	Duodenum Mucosa	Duodenum
33	chr13:50304600-50316000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr13:50305600-50314600	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr13:50305600-50319400	Weak transcription	Fetal Intestine Small	intestine
36	chr13:50305600-50319600	Weak transcription	Fetal Stomach	stomach
37	chr13:50305800-50319400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr13:50305800-50320200	Weak transcription	Fetal Muscle Leg	muscle
39	chr13:50306000-50315000	Weak transcription	Primary T cells from cord blood	blood
40	chr13:50306000-50315000	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr13:50306000-50316600	Weak transcription	Fetal Intestine Large	intestine
42	chr13:50306000-50318400	Weak transcription	Placenta	Placenta
43	chr13:50306000-50319000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr13:50306000-50320200	Weak transcription	Stomach Smooth Muscle	stomach
45	chr13:50306000-50324000	Weak transcription	HSMMtube	muscle
46	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr13:50306200-50316000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr13:50306200-50323200	Weak transcription	Brain Germinal Matrix	brain
49	chr13:50306200-50334200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr13:50306200-50336200	Weak transcription	Adipose Nuclei	Adipose

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