Variant report

Variant	rs12905385
Chromosome Location	chr15:43021563-43021564
allele	A/G
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	chr15:43021525-43021810	K562	blood:	n/a	n/a
2	POLR2A	chr15:43021062-43025465	K562	blood:	n/a	n/a
3	POLR2A	chr15:43021443-43021864	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:43021238-43021673	K562	blood:	n/a	n/a
5	POLR2A	chr15:43021163-43023281	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:43020195..43022907-chr15:43026273..43029275,3	MCF-7	breast:
2	chr15:43019448..43022159-chr15:43025632..43028520,2	MCF-7	breast:
3	chr15:43005044..43007388-chr15:43020446..43022660,2	K562	blood:

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

Extended variants
information (count: 96 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:90)

rs_ID	r²[population]
rs10162939	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1058846	0.89[CEU][hapmap];0.82[MEX][hapmap];0.86[EUR][1000 genomes]
rs1197550	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs1197551	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs12102055	0.90[CEU][hapmap]
rs12902830	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs12903762	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12905592	0.83[EUR][1000 genomes]
rs12906497	0.85[CEU][hapmap]
rs12907826	0.92[EUR][1000 genomes]
rs12911585	0.84[CEU][hapmap];0.82[MEX][hapmap]
rs12913618	0.83[EUR][1000 genomes]
rs12914570	0.84[CEU][hapmap];0.81[LWK][hapmap];0.85[MKK][hapmap]
rs12915116	0.82[MEX][hapmap];0.80[EUR][1000 genomes]
rs12917018	0.81[CEU][hapmap]
rs12917189	0.90[CEU][hapmap];0.80[TSI][hapmap];0.87[EUR][1000 genomes]
rs16957020	0.86[ASW][hapmap];0.82[CEU][hapmap];0.85[CHB][hapmap]
rs16957043	0.83[YRI][hapmap]
rs16957091	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs16957104	0.82[EUR][1000 genomes]
rs16957168	0.93[ASW][hapmap]
rs1705356	0.84[CEU][hapmap]
rs17774047	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs1995939	0.90[CEU][hapmap]
rs2136899	0.93[ASW][hapmap];0.94[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.90[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2136900	0.95[CEU][hapmap];0.85[CHB][hapmap];0.80[EUR][1000 genomes]
rs2136901	0.88[EUR][1000 genomes]
rs2175370	0.84[CEU][hapmap];0.85[CHB][hapmap];0.80[YRI][hapmap];0.82[EUR][1000 genomes]
rs2280048	0.90[CEU][hapmap]
rs2305084	0.85[CEU][hapmap];0.85[CHB][hapmap];0.86[GIH][hapmap];0.84[MKK][hapmap];0.84[EUR][1000 genomes]
rs2305085	0.94[CEU][hapmap];0.85[CHB][hapmap];0.88[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2412741	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs28562951	0.81[EUR][1000 genomes]
rs28744617	0.81[AFR][1000 genomes]
rs3099758	0.84[CEU][hapmap]
rs3199486	0.90[CEU][hapmap]
rs34191150	0.88[EUR][1000 genomes]
rs34603230	0.84[EUR][1000 genomes]
rs35088691	0.82[EUR][1000 genomes]
rs35298309	0.80[EUR][1000 genomes]
rs35392023	0.86[EUR][1000 genomes]
rs35538776	0.82[MEX][hapmap]
rs35616173	0.88[EUR][1000 genomes]
rs3742988	0.90[CEU][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs3742993	0.86[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];0.84[GIH][hapmap];0.83[LWK][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap];0.82[YRI][hapmap];0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4545789	0.84[CEU][hapmap];0.85[CHB][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs4924690	0.83[CEU][hapmap]
rs4924691	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs4924692	0.84[CEU][hapmap];0.85[CHB][hapmap];0.85[EUR][1000 genomes]
rs4924694	0.94[CEU][hapmap];0.85[CHB][hapmap];0.83[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4924699	0.82[MEX][hapmap]
rs4994112	0.95[CEU][hapmap];0.84[TSI][hapmap]
rs57298545	0.84[EUR][1000 genomes]
rs58938096	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61122145	0.86[EUR][1000 genomes]
rs623271	0.84[CEU][hapmap]
rs6493059	0.86[ASW][hapmap];0.84[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes]
rs6493060	0.81[EUR][1000 genomes]
rs6493061	0.89[CEU][hapmap];0.86[EUR][1000 genomes]
rs6493062	0.97[EUR][1000 genomes]
rs6493063	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493066	0.81[AMR][1000 genomes]
rs66681258	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs672054	0.84[CEU][hapmap]
rs7166373	0.84[CEU][hapmap]
rs7167392	0.85[CEU][hapmap];0.82[GIH][hapmap];0.83[LWK][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs7169009	0.90[CEU][hapmap]
rs7174041	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs7175582	0.85[CEU][hapmap];0.83[GIH][hapmap]
rs7176860	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7182141	0.93[ASW][hapmap];0.85[CEU][hapmap];0.83[LWK][hapmap];0.83[MKK][hapmap]
rs7182479	0.88[EUR][1000 genomes]
rs7183487	0.93[EUR][1000 genomes]
rs731984	0.90[CEU][hapmap];0.84[TSI][hapmap];0.92[EUR][1000 genomes]
rs8023524	1.00[CEU][hapmap];0.88[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs8024902	0.84[CEU][hapmap];0.85[CHB][hapmap];0.83[YRI][hapmap];0.84[EUR][1000 genomes]
rs8026233	0.81[CEU][hapmap]
rs8027427	0.81[CEU][hapmap]
rs8028785	0.86[ASW][hapmap]
rs8030587	0.81[EUR][1000 genomes]
rs8031218	0.91[MEX][hapmap];0.82[TSI][hapmap];0.86[EUR][1000 genomes]
rs8034447	0.90[CEU][hapmap];0.84[TSI][hapmap];0.91[EUR][1000 genomes]
rs8039711	0.84[CEU][hapmap];0.85[CHB][hapmap];0.80[YRI][hapmap];0.84[EUR][1000 genomes]
rs8039765	0.84[CEU][hapmap];0.91[MEX][hapmap];0.84[EUR][1000 genomes]
rs8043472	0.84[CEU][hapmap]
rs9269	0.93[ASW][hapmap];0.95[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.95[LWK][hapmap];0.94[MKK][hapmap];0.84[AFR][1000 genomes]
rs938047	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs9919994	0.90[CEU][hapmap]
rs9920163	0.84[CEU][hapmap];0.85[CHB][hapmap]
rs9920182	0.87[ASW][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12905385	CDAN1	cis	parietal	SCAN
rs12905385	BUB1B	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	chr15:43011600-43022800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:43011600-43028000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr15:43011800-43026400	Strong transcription	Primary B cells from peripheral blood	blood
39	chr15:43011800-43027000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr15:43011800-43027800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:43012000-43027200	Strong transcription	Liver	Liver
42	chr15:43012200-43026400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr15:43012600-43026000	Strong transcription	Dnd41	blood
44	chr15:43013400-43021600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr15:43013800-43026000	Strong transcription	Colonic Mucosa	Colon
46	chr15:43013800-43027000	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr15:43013800-43027400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr15:43014000-43027800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr15:43014200-43026800	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr15:43014200-43027600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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