Variant report

Variant	rs2305084
Chromosome Location	chr15:43018691-43018692
allele	A/C
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	chr15:43018686-43019012	HepG2	liver:	n/a	n/a
2	POLR2A	chr15:43018379-43018987	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:43018403-43018845	K562	blood:	n/a	n/a
4	POLR2A	chr15:43018561-43020855	K562	blood:	n/a	n/a
5	POLR2A	chr15:43018537-43019064	K562	blood:	n/a	n/a
6	POLR2A	chr15:43018548-43019893	PANC-1	pancreas:	n/a	n/a
7	POLR2A	chr15:43018534-43019119	PFSK-1	brain:	n/a	n/a

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
CDAN1	TF binding region
ENSG00000140326	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:87)

rs_ID	r²[population]
rs10162939	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs10400824	0.86[EUR][1000 genomes]
rs10518779	1.00[JPT][hapmap];0.92[MEX][hapmap]
rs1197548	0.80[EUR][1000 genomes]
rs1197549	0.80[EUR][1000 genomes]
rs1197550	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs1197551	0.80[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes]
rs12102055	0.85[CEU][hapmap];0.87[EUR][1000 genomes]
rs12905385	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.84[MKK][hapmap];0.84[EUR][1000 genomes]
rs12906497	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs12912064	0.85[EUR][1000 genomes]
rs12914570	0.80[CEU][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap]
rs12917018	0.95[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs12917189	0.85[CEU][hapmap]
rs13329197	0.81[ASN][1000 genomes]
rs16957020	1.00[CHB][hapmap];0.93[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs16957091	0.95[CEU][hapmap];0.86[MEX][hapmap];0.86[TSI][hapmap];0.92[EUR][1000 genomes]
rs16957104	0.91[EUR][1000 genomes]
rs16957168	1.00[JPT][hapmap];0.92[MEX][hapmap];0.90[ASN][1000 genomes]
rs1705356	0.80[CEU][hapmap];0.90[JPT][hapmap]
rs1915241	0.91[EUR][1000 genomes]
rs1995939	0.85[CEU][hapmap];0.85[MEX][hapmap];0.91[EUR][1000 genomes]
rs2136899	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2136900	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2175370	1.00[CHB][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2280048	0.85[CEU][hapmap];0.89[EUR][1000 genomes]
rs2305085	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[YRI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412740	0.89[EUR][1000 genomes]
rs2412741	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs28498538	0.95[ASN][1000 genomes]
rs28549876	0.93[EUR][1000 genomes]
rs28562951	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28620320	0.90[ASN][1000 genomes]
rs28744617	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28798437	0.86[EUR][1000 genomes]
rs28811114	0.85[EUR][1000 genomes]
rs28823029	0.85[EUR][1000 genomes]
rs3099758	0.80[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs3199486	0.85[CEU][hapmap];0.86[MEX][hapmap];0.91[EUR][1000 genomes]
rs34603230	0.85[ASN][1000 genomes]
rs3742987	0.89[CEU][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap];0.94[EUR][1000 genomes]
rs3742988	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs3742993	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs4265781	0.93[EUR][1000 genomes]
rs4545789	1.00[CHB][hapmap]
rs4924690	0.80[CEU][hapmap];0.80[EUR][1000 genomes]
rs4924691	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs4924692	1.00[CHB][hapmap]
rs4924694	0.94[ASW][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.91[LWK][hapmap];0.96[MKK][hapmap];0.85[YRI][hapmap];0.85[AFR][1000 genomes];0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4994112	0.90[CEU][hapmap]
rs623271	0.80[CEU][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes]
rs6493059	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493062	0.84[EUR][1000 genomes]
rs6493063	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6493066	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66681258	0.83[EUR][1000 genomes]
rs672054	0.90[JPT][hapmap]
rs67391479	0.84[EUR][1000 genomes]
rs7163030	0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs7166632	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7166775	0.90[CEU][hapmap];0.83[TSI][hapmap];0.89[EUR][1000 genomes]
rs7167392	1.00[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169009	0.95[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs7169202	0.82[EUR][1000 genomes]
rs7174041	0.84[CEU][hapmap]
rs7175582	1.00[ASW][hapmap];0.80[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7176860	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7182141	0.80[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7182515	1.00[JPT][hapmap]
rs731984	0.85[CEU][hapmap]
rs8023524	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8024902	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs8026233	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs8027427	0.95[CEU][hapmap];0.93[EUR][1000 genomes]
rs8028785	1.00[JPT][hapmap];0.92[MEX][hapmap]
rs8034447	0.85[CEU][hapmap];0.80[EUR][1000 genomes]
rs8034664	0.89[EUR][1000 genomes]
rs8039711	1.00[CHB][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs8039765	0.90[JPT][hapmap]
rs8043472	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs9269	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs938047	0.90[JPT][hapmap]
rs9783713	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9919994	0.85[CEU][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.82[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9920163	0.80[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9920182	0.85[MEX][hapmap]
rs9920202	1.00[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	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
rs2305084	SPTBN5	cis	cerebellum	SCAN
rs2305084	CDAN1	cis	parietal	SCAN
rs2305084	CHAC1	cis	parietal	SCAN

Chromatin state (count:125 , 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	chr15:43007800-43020800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:43008000-43027600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr15:43008200-43027600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr15:43008200-43027800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr15:43008400-43020000	Strong transcription	Fetal Muscle Trunk	muscle
7	chr15:43008400-43020400	Strong transcription	Brain Substantia Nigra	brain
8	chr15:43008600-43027400	Strong transcription	Fetal Brain Female	brain
9	chr15:43008800-43019800	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr15:43008800-43026600	Strong transcription	Skeletal Muscle Male	skeletal muscle
11	chr15:43008800-43027200	Strong transcription	Brain Germinal Matrix	brain
12	chr15:43008800-43027200	Strong transcription	Lung	lung
13	chr15:43008800-43027400	Strong transcription	Adipose Nuclei	Adipose
14	chr15:43008800-43027800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr15:43009000-43027400	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:43009000-43027600	Strong transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:43009000-43027800	Strong transcription	Fetal Intestine Large	intestine
18	chr15:43009200-43027800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:43009600-43026600	Strong transcription	Spleen	Spleen
20	chr15:43009600-43027400	Strong transcription	Fetal Intestine Small	intestine
21	chr15:43009600-43027800	Strong transcription	Left Ventricle	heart
22	chr15:43009800-43020800	Weak transcription	Stomach Mucosa	stomach
23	chr15:43010000-43020200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr15:43010000-43027200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:43010000-43027400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr15:43010000-43027600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:43010000-43027600	Strong transcription	Brain Anterior Caudate	brain
28	chr15:43010000-43027600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr15:43010200-43027400	Strong transcription	Primary T cells from cord blood	blood
30	chr15:43010200-43027600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr15:43010200-43027600	Strong transcription	Ovary	ovary
32	chr15:43010200-43027800	Strong transcription	Gastric	stomach
33	chr15:43010400-43026800	Strong transcription	Stomach Smooth Muscle	stomach
34	chr15:43010400-43026800	Strong transcription	Thymus	Thymus
35	chr15:43010400-43027600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:43010400-43027800	Strong transcription	Placenta	Placenta
37	chr15:43010800-43020600	Strong transcription	Fetal Lung	lung
38	chr15:43011000-43026600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr15:43011000-43026800	Strong transcription	Rectal Mucosa Donor 31	rectum
40	chr15:43011000-43027200	Strong transcription	Duodenum Mucosa	Duodenum
41	chr15:43011200-43020400	Strong transcription	Primary B cells from cord blood	blood
42	chr15:43011200-43027600	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr15:43011400-43027600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr15:43011600-43019800	Weak transcription	Fetal Heart	heart
45	chr15:43011600-43022800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr15:43011600-43028000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr15:43011800-43026400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr15:43011800-43027000	Strong transcription	Primary neutrophils fromperipheralblood	blood
49	chr15:43011800-43027800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
50	chr15:43012000-43027200	Strong transcription	Liver	Liver

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