Variant report

Variant	rs16957091
Chromosome Location	chr15:43017426-43017427
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43014319..43018768-chr15:43027782..43030873,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:89)

rs_ID	r²[population]
rs10400824	0.81[EUR][1000 genomes]
rs11070374	1.00[YRI][hapmap]
rs1206698	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12102055	0.90[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12594483	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes]
rs12594855	0.94[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12594951	0.87[ASW][hapmap]
rs12905385	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs12905592	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs12906497	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12907826	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12912064	0.90[EUR][1000 genomes]
rs12917018	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12917189	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16957020	0.82[EUR][1000 genomes]
rs16957104	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1705356	0.91[GIH][hapmap];0.93[MEX][hapmap]
rs1915241	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1995939	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2136900	0.85[CEU][hapmap];0.90[EUR][1000 genomes]
rs2136901	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2280048	0.90[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2305084	0.95[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs2305085	0.83[CEU][hapmap];0.82[EUR][1000 genomes]
rs2412740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2412741	0.90[CEU][hapmap];0.95[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28479391	0.87[ASN][1000 genomes]
rs28549876	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28562951	0.89[EUR][1000 genomes]
rs28798437	0.81[EUR][1000 genomes]
rs28811114	0.81[EUR][1000 genomes]
rs28823029	0.81[EUR][1000 genomes]
rs3099758	0.93[GIH][hapmap];0.93[MEX][hapmap]
rs3199486	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34191150	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35616173	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35738819	0.96[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs3742987	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3742988	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4265781	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4923950	0.96[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4924690	0.89[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4924691	0.82[EUR][1000 genomes]
rs4994112	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap]
rs623271	0.91[GIH][hapmap];0.86[MEX][hapmap]
rs6493059	0.86[MEX][hapmap];0.83[EUR][1000 genomes]
rs6493060	1.00[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.85[MEX][hapmap];1.00[YRI][hapmap];0.91[ASN][1000 genomes]
rs6493061	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6493062	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6493063	0.93[EUR][1000 genomes]
rs6493066	0.82[EUR][1000 genomes]
rs6493067	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs6493068	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap]
rs66681258	0.83[EUR][1000 genomes]
rs67391479	0.88[EUR][1000 genomes]
rs7163030	0.81[CEU][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs7166373	0.95[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs7166632	0.83[EUR][1000 genomes]
rs7166775	1.00[ASW][hapmap];0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167392	0.95[CEU][hapmap];0.85[TSI][hapmap];0.92[EUR][1000 genomes]
rs7167802	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7168835	1.00[YRI][hapmap]
rs7169009	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7169202	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7174041	0.89[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7175582	0.89[EUR][1000 genomes]
rs7182141	0.89[EUR][1000 genomes]
rs7182479	0.81[EUR][1000 genomes]
rs7182753	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs731984	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023524	0.81[CEU][hapmap];0.81[EUR][1000 genomes]
rs8026233	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8027427	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8030587	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.86[ASN][1000 genomes]
rs8031218	0.81[GIH][hapmap]
rs8034447	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.98[GIH][hapmap];0.83[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034664	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8035752	1.00[ASW][hapmap]
rs8036096	1.00[ASW][hapmap]
rs8039765	0.85[GIH][hapmap]
rs8043472	1.00[ASW][hapmap];0.91[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs9269	0.85[CEU][hapmap];0.86[MEX][hapmap];0.80[TSI][hapmap];0.91[EUR][1000 genomes]
rs9783683	1.00[YRI][hapmap]
rs9783713	0.89[EUR][1000 genomes]
rs9806175	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs9919994	0.90[CEU][hapmap];0.89[GIH][hapmap];0.90[EUR][1000 genomes]
rs9920163	0.81[EUR][1000 genomes]
rs9920182	0.88[JPT][hapmap];0.86[MEX][hapmap]
rs9944248	0.83[AFR][1000 genomes];0.83[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	nsv528725	chr15:42755555-43104406	Weak transcription Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv427959	chr15:42931181-43207353	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv457122	chr15:42948862-43062548	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv569238	chr15:42948862-43062548	Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
5	nsv517553	chr15:42970899-43023482	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	3 gene(s)	inside rSNPs	diseases
6	nsv977054	chr15:43015821-43171355	Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16957091	BUB1B	cis	parietal	SCAN
rs16957091	CDAN1	cis	parietal	SCAN
rs16957091	TGM5	cis	lymphoblastoid	seeQTL
rs16957091	MAP1A	cis	parietal	SCAN
rs16957091	SPTBN5	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42986000-43018400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:43000800-43018600	Weak transcription	A549	lung
3	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
4	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
9	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
10	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
11	chr15:43008800-43018400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
13	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
14	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
15	chr15:43008800-43027200	Strong transcription	Lung	lung
16	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
17	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
20	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
21	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:43009400-43018200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
24	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine
25	chr15:43009600-43027800	Strong transcription	Left Ventricle	heart
26	chr15:43009800-43018600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:43009800-43020800	Weak transcription	Stomach Mucosa	stomach
28	chr15:43010000-43020200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
29	chr15:43010000-43027200	Strong transcription	Skeletal Muscle Female	skeletal muscle
30	chr15:43010000-43027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr15:43010000-43027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:43010000-43027600	Strong transcription	Brain Anterior Caudate	brain
33	chr15:43010000-43027600	Strong transcription	Rectal Mucosa Donor 29	rectum
34	chr15:43010200-43027400	Strong transcription	Primary T cells from cord blood	blood
35	chr15:43010200-43027600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr15:43010200-43027600	Strong transcription	Ovary	ovary
37	chr15:43010200-43027800	Strong transcription	Gastric	stomach
38	chr15:43010400-43026800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr15:43010400-43026800	Strong transcription	Thymus	Thymus
40	chr15:43010400-43027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:43010400-43027800	Strong transcription	Placenta	Placenta
42	chr15:43010800-43020600	Strong transcription	Fetal Lung	lung
43	chr15:43011000-43026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr15:43011000-43026800	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr15:43011000-43027200	Strong transcription	Duodenum Mucosa	Duodenum
46	chr15:43011200-43020400	Strong transcription	Primary B cells from cord blood	blood
47	chr15:43011200-43027600	Strong transcription	Primary monocytes fromperipheralblood	blood
48	chr15:43011400-43027600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr15:43011600-43019800	Weak transcription	Fetal Heart	heart
50	chr15:43011600-43022800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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