Variant report

Variant	rs1678409
Chromosome Location	chr13:95718488-95718489
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	chr13:95713683..95715705-chr13:95717274..95719988,2	MCF-7	breast:

Extended variants
information (count: 76 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1151471	0.81[JPT][hapmap]
rs1189430	0.86[EUR][1000 genomes]
rs1189431	0.86[EUR][1000 genomes]
rs1189433	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1189434	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.84[MKK][hapmap];0.88[TSI][hapmap];0.88[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1189435	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1189436	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1189437	1.00[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1189438	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes]
rs1189439	1.00[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1189440	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1189441	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1189442	0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.91[ASN][1000 genomes]
rs1189443	0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1189444	0.93[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs1189445	0.90[JPT][hapmap]
rs1189446	0.90[JPT][hapmap]
rs1189449	0.90[JPT][hapmap]
rs1189451	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs1189452	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.93[ASN][1000 genomes]
rs1189453	0.89[ASN][1000 genomes]
rs1189454	0.80[ASN][1000 genomes]
rs1189456	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1189461	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189462	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1189463	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1189464	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1189466	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1189467	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1612388	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1629441	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1630901	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1678339	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1678341	0.87[CHD][hapmap]
rs1678347	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1678351	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1678353	1.00[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.86[EUR][1000 genomes]
rs1678362	1.00[CEU][hapmap];0.90[CHD][hapmap];0.90[GIH][hapmap];0.86[JPT][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs1678365	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678387	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1678395	0.90[CHD][hapmap];0.85[JPT][hapmap]
rs1729745	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1729747	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1729752	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1729753	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1729755	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1729773	1.00[CEU][hapmap];0.85[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1751031	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1751033	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1751034	0.96[ASN][1000 genomes]
rs1751036	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1751037	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1751042	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1751043	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1751046	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1751052	0.90[CHD][hapmap];0.86[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs1751055	1.00[CEU][hapmap];0.84[JPT][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1751056	0.85[EUR][1000 genomes]
rs1751057	1.00[CEU][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2619308	0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2619311	0.91[JPT][hapmap]
rs2619312	0.86[CHB][hapmap];0.93[CHD][hapmap];0.91[JPT][hapmap];0.92[ASN][1000 genomes]
rs2766475	1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2950957	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4148540	0.82[CEU][hapmap];0.86[CHB][hapmap];0.80[CHD][hapmap];1.00[GIH][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap]
rs4773840	0.86[CHD][hapmap]
rs7330330	0.82[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap]
rs7331488	0.82[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap];0.88[YRI][hapmap]
rs7338853	0.93[ASN][1000 genomes]
rs7986666	0.83[ASN][1000 genomes]
rs931111	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs943289	1.00[CEU][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9524790	0.93[ASN][1000 genomes]
rs9561765	0.82[CEU][hapmap];0.84[GIH][hapmap];0.94[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832688	chr13:95633193-95780198	Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
2	nsv525194	chr13:95672950-95737192	Strong transcription Enhancers Weak transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:95655600-95722600	Weak transcription	Gastric	stomach
2	chr13:95669400-95723200	Weak transcription	Primary hematopoietic stem cells	blood
3	chr13:95669600-95744000	Weak transcription	Small Intestine	intestine
4	chr13:95671400-95722200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr13:95672800-95729000	Weak transcription	Colonic Mucosa	Colon
6	chr13:95676000-95740000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr13:95682800-95721800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:95683200-95751800	Weak transcription	Fetal Lung	lung
9	chr13:95683800-95725800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr13:95684400-95728200	Weak transcription	Adipose Nuclei	Adipose
11	chr13:95684600-95725400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr13:95685000-95721400	Weak transcription	Fetal Intestine Small	intestine
13	chr13:95685200-95734600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr13:95686800-95722600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr13:95686800-95744600	Weak transcription	Esophagus	oesophagus
16	chr13:95687000-95722600	Weak transcription	Rectal Mucosa Donor 31	rectum
17	chr13:95691200-95722400	Weak transcription	Fetal Stomach	stomach
18	chr13:95692000-95722400	Weak transcription	Spleen	Spleen
19	chr13:95692200-95722800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr13:95692600-95721200	Weak transcription	Ovary	ovary
21	chr13:95692600-95725600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr13:95692800-95735800	Weak transcription	NHEK	skin
23	chr13:95693800-95722600	Weak transcription	Fetal Intestine Large	intestine
24	chr13:95694400-95718800	Weak transcription	Stomach Smooth Muscle	stomach
25	chr13:95694800-95721000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr13:95694800-95721800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr13:95694800-95725600	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr13:95695000-95722000	Weak transcription	Lung	lung
29	chr13:95695000-95722200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
30	chr13:95695200-95719000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr13:95695600-95723800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr13:95695800-95721200	Weak transcription	Duodenum Mucosa	Duodenum
33	chr13:95696000-95726200	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr13:95702400-95735200	Weak transcription	Primary T helper cells PMA-I stimulated	--
35	chr13:95706000-95719200	Weak transcription	HUVEC	blood vessel
36	chr13:95709200-95728000	Weak transcription	HSMMtube	muscle
37	chr13:95710000-95723600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:95710200-95727400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr13:95710400-95741200	Weak transcription	Right Ventricle	heart
40	chr13:95711200-95721400	Weak transcription	Aorta	Aorta
41	chr13:95711600-95718800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:95711800-95719000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr13:95711800-95719600	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr13:95711800-95724600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr13:95712200-95723400	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr13:95712800-95719200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr13:95712800-95721000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr13:95713000-95727000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr13:95713200-95719800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr13:95713200-95722000	Weak transcription	Skeletal Muscle Male	skeletal muscle

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