Variant report

Variant	rs12917189
Chromosome Location	chr15:43023482-43023483
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:43022767-43023538	SK-N-MC	brain:	n/a	n/a
2	POLR2A	chr15:43023328-43024072	K562	blood:	n/a	n/a
3	POLR2A	chr15:43023209-43023629	GM12878	blood:	n/a	n/a
4	ZNF263	chr15:43022685-43023536	HEK293-T-REx	kidney:	n/a	n/a
5	POLR2A	chr15:43022258-43024033	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:43023352-43024197	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr15:43021062-43025465	K562	blood:	n/a	n/a
8	POLR2A	chr15:43023463-43023524	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43023409..43026970-chr15:43028555..43030726,4	MCF-7	breast:

Variant related genes	Relation type
CDAN1	TF binding region
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs11070374	1.00[YRI][hapmap]
rs1206698	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs12102055	0.90[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12594483	1.00[ASW][hapmap];1.00[LWK][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes]
rs12594855	0.94[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12594951	0.87[ASW][hapmap]
rs12903762	0.85[EUR][1000 genomes]
rs12905385	0.90[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs12905592	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12906497	0.85[CEU][hapmap];0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12907826	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12913618	0.80[EUR][1000 genomes]
rs12917018	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16957091	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]
rs16957104	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1705356	0.82[GIH][hapmap];0.85[MEX][hapmap]
rs1915241	0.93[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1995939	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2136899	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs2136900	0.84[CEU][hapmap]
rs2136901	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2280048	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2305084	0.85[CEU][hapmap]
rs2305085	0.94[CEU][hapmap];0.87[EUR][1000 genomes]
rs2412740	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2412741	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28479391	0.85[ASN][1000 genomes]
rs28549876	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3099758	0.84[GIH][hapmap];0.85[MEX][hapmap]
rs3199486	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs34191150	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35616173	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35738819	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3742987	0.84[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3742988	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742993	0.80[EUR][1000 genomes]
rs4265781	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4923950	0.89[AFR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4924690	0.89[CHB][hapmap];0.85[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs4924694	0.84[CEU][hapmap];0.83[MEX][hapmap];0.84[EUR][1000 genomes]
rs4994112	1.00[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap]
rs58938096	0.85[EUR][1000 genomes]
rs623271	0.82[GIH][hapmap]
rs6493060	1.00[ASW][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6493061	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6493062	0.93[AMR][1000 genomes];0.88[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	0.90[EUR][1000 genomes]
rs7163030	0.87[GIH][hapmap]
rs7166373	0.95[CHB][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7166775	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs7167392	0.85[CEU][hapmap]
rs7167802	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7168835	1.00[YRI][hapmap]
rs7169009	1.00[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.85[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169202	1.00[CHB][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7174041	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7176860	0.84[EUR][1000 genomes]
rs7182479	0.87[EUR][1000 genomes]
rs7182753	1.00[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap]
rs7183487	0.85[EUR][1000 genomes]
rs731984	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8023524	0.90[CEU][hapmap];0.86[EUR][1000 genomes]
rs8026233	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8027427	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8030587	1.00[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];0.87[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8031218	0.84[MEX][hapmap]
rs8034447	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8034664	0.89[ASN][1000 genomes]
rs8035752	1.00[ASW][hapmap]
rs8036096	1.00[ASW][hapmap]
rs8039765	0.81[GIH][hapmap];0.84[MEX][hapmap]
rs8043472	1.00[ASW][hapmap];0.82[GIH][hapmap];0.85[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs9269	0.84[CEU][hapmap]
rs9783683	1.00[YRI][hapmap]
rs9806175	1.00[ASW][hapmap];1.00[LWK][hapmap]
rs9919994	0.90[CEU][hapmap];0.81[GIH][hapmap]
rs9920182	0.94[JPT][hapmap]
rs9944248	0.80[EUR][1000 genomes];0.80[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12917189	BUB1B	cis	parietal	SCAN
rs12917189	CDAN1	cis	parietal	SCAN
rs12917189	MAP1A	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43007200-43026800	Strong transcription	Fetal Stomach	stomach
2	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
3	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
6	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
8	chr15:43008800-43027200	Strong transcription	Lung	lung
9	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
10	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
13	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
14	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
16	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine
17	chr15:43009600-43027800	Strong transcription	Left Ventricle	heart
18	chr15:43010000-43027200	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr15:43010000-43027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr15:43010000-43027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr15:43010000-43027600	Strong transcription	Brain Anterior Caudate	brain
22	chr15:43010000-43027600	Strong transcription	Rectal Mucosa Donor 29	rectum
23	chr15:43010200-43027400	Strong transcription	Primary T cells from cord blood	blood
24	chr15:43010200-43027600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr15:43010200-43027600	Strong transcription	Ovary	ovary
26	chr15:43010200-43027800	Strong transcription	Gastric	stomach
27	chr15:43010400-43026800	Strong transcription	Stomach Smooth Muscle	stomach
28	chr15:43010400-43026800	Strong transcription	Thymus	Thymus
29	chr15:43010400-43027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:43010400-43027800	Strong transcription	Placenta	Placenta
31	chr15:43011000-43026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr15:43011000-43026800	Strong transcription	Rectal Mucosa Donor 31	rectum
33	chr15:43011000-43027200	Strong transcription	Duodenum Mucosa	Duodenum
34	chr15:43011200-43027600	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr15:43011400-43027600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:43011600-43028000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr15:43011800-43026400	Strong transcription	Primary B cells from peripheral blood	blood
38	chr15:43011800-43027000	Strong transcription	Primary neutrophils fromperipheralblood	blood
39	chr15:43011800-43027800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:43012000-43027200	Strong transcription	Liver	Liver
41	chr15:43012200-43026400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
42	chr15:43012600-43026000	Strong transcription	Dnd41	blood
43	chr15:43013800-43026000	Strong transcription	Colonic Mucosa	Colon
44	chr15:43013800-43027000	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr15:43013800-43027400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:43014000-43027800	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr15:43014200-43026800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:43014200-43027600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr15:43014200-43027800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:43014400-43027600	Strong transcription	Right Ventricle	heart

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