Variant report

Variant	rs9596194
Chromosome Location	chr13:50350340-50350341
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:50349733..50352662-chr13:50364217..50367183,2	MCF-7	breast:
2	chr13:50344680..50346615-chr13:50348215..50350445,3	K562	blood:
3	chr13:50349371..50350894-chr13:50365184..50367283,2	MCF-7	breast:
4	chr13:50344891..50347540-chr13:50347984..50350417,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000102753	Chromatin interaction

Extended variants
information (count: 62 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1043729	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12585836	0.87[EUR][1000 genomes]
rs12585921	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13313256	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17073322	0.92[EUR][1000 genomes]
rs17073347	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17073356	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1819191	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1885723	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1986085	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1998363	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2181184	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2236326	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2407875	0.88[EUR][1000 genomes]
rs3742094	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3782929	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3903770	0.88[EUR][1000 genomes]
rs3990324	0.96[ASN][1000 genomes]
rs4941655	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4941656	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4942862	0.92[EUR][1000 genomes]
rs4942865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56738401	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57118905	0.92[EUR][1000 genomes]
rs57783887	0.84[EUR][1000 genomes]
rs57794226	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58124341	0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59823147	0.84[EUR][1000 genomes]
rs60019803	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60106669	0.84[EUR][1000 genomes]
rs60856213	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7321391	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7326885	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7334018	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7335016	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7335310	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73483835	0.84[EUR][1000 genomes]
rs73485710	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs765291	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs765292	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7984711	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7989633	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7993631	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7993860	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7994062	0.90[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9591293	0.82[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9591294	0.83[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9591296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596172	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9596173	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9596174	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9596175	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9596176	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9596181	0.83[AFR][1000 genomes]
rs9596188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9596189	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][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

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50306000-50351600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr13:50308000-50356000	Weak transcription	Fetal Kidney	kidney
3	chr13:50321000-50363800	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr13:50324600-50350800	Weak transcription	HSMM	muscle
5	chr13:50324600-50351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr13:50334000-50352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr13:50334200-50351200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:50334400-50350800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr13:50334400-50351400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr13:50335000-50356400	Weak transcription	Primary B cells from cord blood	blood
11	chr13:50336200-50364800	Weak transcription	Fetal Intestine Small	intestine
12	chr13:50336400-50351600	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr13:50336600-50352400	Weak transcription	Thymus	Thymus
14	chr13:50336600-50353800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:50336800-50364600	Weak transcription	NHLF	lung
16	chr13:50338000-50353800	Weak transcription	Dnd41	blood
17	chr13:50339200-50353800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr13:50339200-50355800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr13:50339200-50358800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr13:50339800-50358800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr13:50340600-50351200	Weak transcription	A549	lung
22	chr13:50341200-50359400	Weak transcription	Primary hematopoietic stem cells	blood
23	chr13:50343400-50351800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr13:50344000-50355600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr13:50345400-50351200	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr13:50345800-50351400	Weak transcription	GM12878-XiMat	blood
27	chr13:50346000-50351600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr13:50346200-50351600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
29	chr13:50347000-50351600	Weak transcription	Psoas Muscle	Psoas
30	chr13:50348600-50351600	Enhancers	Liver	Liver
31	chr13:50349000-50350400	Enhancers	Ovary	ovary
32	chr13:50349200-50351600	Weak transcription	Pancreas	Pancrea
33	chr13:50349600-50352400	Weak transcription	Right Atrium	heart
34	chr13:50349600-50353600	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr13:50349600-50357600	Weak transcription	Gastric	stomach
36	chr13:50349600-50357600	Weak transcription	Left Ventricle	heart
37	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr13:50349600-50365400	Weak transcription	Lung	lung
39	chr13:50349800-50351000	Weak transcription	NHDF-Ad	bronchial
40	chr13:50349800-50351800	Weak transcription	HepG2	liver
41	chr13:50349800-50355200	Weak transcription	Fetal Heart	heart
42	chr13:50350000-50350400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
43	chr13:50350000-50350600	Enhancers	Primary T helper cells fromperipheralblood	blood
44	chr13:50350000-50351000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr13:50350000-50353800	Weak transcription	Brain Substantia Nigra	brain
46	chr13:50350200-50351200	Weak transcription	Stomach Mucosa	stomach
47	chr13:50350200-50351800	Weak transcription	Primary T helper cells PMA-I stimulated	--
48	chr13:50350200-50352600	Enhancers	Primary T helper naive cells from peripheral blood	blood

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