Variant report

Variant	rs9646001
Chromosome Location	chr13:50347710-50347711
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	chr13:50346317..50348509-chr13:50365668..50368332,3	MCF-7	breast:
2	chr13:50339282..50341769-chr13:50347663..50349184,2	K562	blood:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs11148160	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11148161	0.90[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11148163	0.83[AMR][1000 genomes]
rs11148164	0.83[JPT][hapmap]
rs11148167	0.86[CEU][hapmap];0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12428108	0.82[JPT][hapmap]
rs12584401	0.92[JPT][hapmap]
rs12584560	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12866447	0.86[CEU][hapmap];0.91[JPT][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12868235	0.83[ASN][1000 genomes]
rs12869900	0.88[EUR][1000 genomes]
rs12876223	0.85[EUR][1000 genomes]
rs1535543	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1575387	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1581744	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1923730	0.86[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2146143	0.82[JPT][hapmap]
rs2236354	0.91[JPT][hapmap];0.83[AMR][1000 genomes]
rs3742095	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4643206	0.91[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4941657	0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs4942864	0.82[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6561552	0.82[JPT][hapmap]
rs7446	0.82[JPT][hapmap]
rs7987502	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7997798	0.86[CEU][hapmap];0.91[JPT][hapmap]
rs9526592	0.90[JPT][hapmap]
rs9526595	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9526600	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535301	0.82[JPT][hapmap]
rs9535302	0.84[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9535309	0.90[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9535326	0.86[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9535332	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535333	0.87[CEU][hapmap];0.92[JPT][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535337	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535339	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9535347	0.91[JPT][hapmap]

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
rs9646001	KPNA3	Cis_1M	lymphoblastoid	RTeQTL
rs9646001	EBPL	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50266400-50349000	Weak transcription	Esophagus	oesophagus
2	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
3	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
4	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr13:50324600-50350800	Weak transcription	HSMM	muscle
6	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr13:50326200-50349000	Weak transcription	Left Ventricle	heart
8	chr13:50328400-50349000	Weak transcription	Lung	lung
9	chr13:50328600-50349000	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr13:50330800-50349000	Weak transcription	HepG2	liver
11	chr13:50334000-50352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr13:50334200-50351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:50334400-50350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr13:50334400-50351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
15	chr13:50334600-50350200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
17	chr13:50335200-50349400	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
19	chr13:50336400-50351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr13:50336600-50352400	Weak transcription	Thymus	Thymus
21	chr13:50336600-50353800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr13:50336800-50364600	Weak transcription	NHLF	lung
23	chr13:50338000-50349800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr13:50338000-50353800	Weak transcription	Dnd41	blood
25	chr13:50339200-50353800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr13:50340600-50351200	Weak transcription	A549	lung
30	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
31	chr13:50343400-50351800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr13:50344000-50355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:50345400-50351200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr13:50345800-50351400	Weak transcription	GM12878-XiMat	blood
35	chr13:50346000-50349000	Weak transcription	Ovary	ovary
36	chr13:50346000-50351600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr13:50346200-50351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr13:50347000-50351600	Weak transcription	Psoas Muscle	Psoas

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