Variant report

Variant	rs7984061
Chromosome Location	chr13:50337340-50337341
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:50337068..50338676-chr13:50348072..50349977,2	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1009333	0.81[EUR][1000 genomes]
rs10492591	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1127021	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1198315	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1198319	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1198320	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1198322	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1198324	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1201716	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs1211304	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1407440	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1407441	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1547623	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1570353	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1581745	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1885724	0.80[AFR][1000 genomes]
rs2025263	0.84[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2146143	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs2181185	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2407804	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2897770	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3851162	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4942863	1.00[CEU][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4942866	0.81[AMR][1000 genomes]
rs61961491	0.81[AMR][1000 genomes]
rs6561552	0.93[CEU][hapmap];0.86[YRI][hapmap]
rs6561560	0.92[CEU][hapmap]
rs7330392	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7983303	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9316474	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9526591	0.90[EUR][1000 genomes]
rs9526593	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535305	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9535307	1.00[CEU][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535310	1.00[CEU][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535316	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9535330	0.88[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs9535340	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9535341	0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9562927	0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1038	chr13:50324773-50359990	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	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
rs7984061	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs7984061	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50296600-50338600	Weak transcription	Ovary	ovary
3	chr13:50300600-50345600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
6	chr13:50317600-50343600	Weak transcription	Primary T cells from cord blood	blood
7	chr13:50320600-50337400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr13:50320600-50337800	Weak transcription	Fetal Muscle Trunk	muscle
9	chr13:50320800-50340400	Weak transcription	HUVEC	blood vessel
10	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr13:50324400-50340400	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr13:50324600-50350800	Weak transcription	HSMM	muscle
13	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:50324800-50338600	Weak transcription	Right Atrium	heart
15	chr13:50326200-50349000	Weak transcription	Left Ventricle	heart
16	chr13:50328200-50338600	Weak transcription	Right Ventricle	heart
17	chr13:50328400-50338600	Weak transcription	Pancreas	Pancrea
18	chr13:50328400-50349000	Weak transcription	Lung	lung
19	chr13:50328600-50349000	Weak transcription	Skeletal Muscle Female	skeletal muscle
20	chr13:50330800-50349000	Weak transcription	HepG2	liver
21	chr13:50333400-50338800	Weak transcription	Fetal Heart	heart
22	chr13:50334000-50338000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr13:50334000-50352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr13:50334200-50351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr13:50334400-50337400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr13:50334400-50350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr13:50334400-50351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr13:50334600-50350200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr13:50334800-50337600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
31	chr13:50335200-50337800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr13:50335200-50339800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr13:50335200-50341800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr13:50335200-50342800	Weak transcription	GM12878-XiMat	blood
35	chr13:50335200-50347200	Weak transcription	Primary B cells from peripheral blood	blood
36	chr13:50335200-50349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr13:50335400-50339800	Weak transcription	Primary hematopoietic stem cells	blood
38	chr13:50335400-50339800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
39	chr13:50335400-50340000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr13:50335400-50343000	Weak transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:50335600-50337800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr13:50336200-50339800	Weak transcription	Fetal Stomach	stomach
43	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
44	chr13:50336400-50341600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:50336400-50351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr13:50336600-50337600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr13:50336600-50337800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr13:50336600-50339200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr13:50336600-50340600	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr13:50336600-50352400	Weak transcription	Thymus	Thymus

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