Variant report

Variant	rs16957385
Chromosome Location	chr15:43357416-43357417
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:43356222..43358202-chr15:43362263..43364733,2	MCF-7	breast:

Extended variants
information (count: 96 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs1037990	0.90[EUR][1000 genomes]
rs11070386	1.00[CEU][hapmap];0.93[JPT][hapmap];0.92[EUR][1000 genomes]
rs11070387	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11070388	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11070391	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap]
rs11070396	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs11630595	1.00[CEU][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11855754	0.89[CEU][hapmap]
rs12050596	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12592725	0.89[CEU][hapmap]
rs12899266	1.00[CEU][hapmap];0.87[JPT][hapmap]
rs12905967	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12913617	0.92[EUR][1000 genomes]
rs1381856	0.86[EUR][1000 genomes]
rs1462856	1.00[CEU][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs16957244	1.00[CEU][hapmap];0.84[GIH][hapmap];0.94[MEX][hapmap]
rs16957250	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs16957264	0.88[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap]
rs16957511	0.89[CEU][hapmap]
rs1972447	0.81[EUR][1000 genomes]
rs1993813	0.85[EUR][1000 genomes]
rs1996675	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2035170	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2037392	0.80[CEU][hapmap]
rs2054389	0.86[EUR][1000 genomes]
rs2126602	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2241516	0.89[CEU][hapmap]
rs2412746	0.85[EUR][1000 genomes]
rs2412747	0.85[EUR][1000 genomes]
rs2412752	0.93[JPT][hapmap]
rs2682073	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs28585036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2899069	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2899077	0.89[CEU][hapmap];0.87[MEX][hapmap]
rs2947019	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs3736054	0.93[JPT][hapmap];0.82[MEX][hapmap];0.83[AMR][1000 genomes]
rs3784265	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3803341	1.00[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs4338775	0.85[EUR][1000 genomes]
rs4509988	0.85[EUR][1000 genomes]
rs4573908	1.00[CEU][hapmap];0.93[JPT][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4923955	1.00[CEU][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs4924701	0.84[EUR][1000 genomes]
rs4924704	1.00[CEU][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs494863	0.89[CEU][hapmap]
rs495286	0.89[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap]
rs497138	0.88[CEU][hapmap]
rs530305	0.89[CEU][hapmap]
rs531850	0.89[CEU][hapmap]
rs538218	0.89[CEU][hapmap];0.85[MEX][hapmap]
rs540587	1.00[CEU][hapmap]
rs55805543	0.80[EUR][1000 genomes]
rs6416436	0.85[EUR][1000 genomes]
rs6493076	1.00[CEU][hapmap];0.84[GIH][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6493077	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7174028	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap]
rs7174915	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap]
rs7176116	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7178567	1.00[CEU][hapmap];0.86[GIH][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes]
rs7183814	0.89[CEU][hapmap]
rs8027371	0.80[CEU][hapmap]
rs8027733	1.00[CEU][hapmap];0.93[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs8031767	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes]
rs8035894	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8036710	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8037022	1.00[CEU][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs8042481	1.00[CEU][hapmap];0.87[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes]
rs9796571	0.81[EUR][1000 genomes]
rs9920498	0.88[EUR][1000 genomes]
rs9920904	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525461	chr15:43062548-43482127	Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
2	nsv1044522	chr15:43115348-43658417	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
3	nsv515876	chr15:43116906-43445305	Strong transcription Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
4	nsv904135	chr15:43143998-43392075	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv569239	chr15:43201109-43392075	Strong transcription Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv569240	chr15:43201109-43445305	Weak transcription Strong transcription Bivalent/Poised TSS Flanking Active TSS Enhancers Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	nsv569241	chr15:43201109-43522922	Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1039587	chr15:43204351-43378274	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv569242	chr15:43210030-43445305	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
10	nsv1050987	chr15:43237103-43385515	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	nsv542369	chr15:43237103-43385515	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv904136	chr15:43257475-43482127	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
13	nsv904137	chr15:43268970-43392075	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv904138	chr15:43268970-43414673	Strong transcription Enhancers Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
15	nsv904139	chr15:43268970-43482127	Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers Enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
16	nsv1044508	chr15:43270637-43658417	Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
17	nsv904140	chr15:43276345-43385147	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
18	nsv904141	chr15:43276345-43392075	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
19	nsv904142	chr15:43276345-43403955	Strong transcription Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
20	nsv904143	chr15:43276345-43414673	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
21	nsv904144	chr15:43276345-43482127	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
22	esv3384283	chr15:43280479-43380788	Strong transcription Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
23	nsv904145	chr15:43286746-43392075	Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
24	nsv904146	chr15:43294218-43414673	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
25	nsv1048937	chr15:43299522-43357631	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
26	nsv904147	chr15:43309429-43403955	Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16957385	CCNDBP1	cis	multi-tissue	Pritchard
rs16957385	TGM5	cis	lymphoblastoid	seeQTL
rs16957385	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs16957385	TTBK2	cis	parietal	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:43232000-43362800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:43269200-43397200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:43301800-43385800	Weak transcription	Gastric	stomach
4	chr15:43303400-43397400	Weak transcription	Esophagus	oesophagus
5	chr15:43322600-43376200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:43333000-43367400	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr15:43333000-43367400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:43333400-43367200	Strong transcription	Primary B cells from peripheral blood	blood
9	chr15:43333400-43367400	Strong transcription	Primary T cells fromperipheralblood	blood
10	chr15:43333400-43367400	Strong transcription	Adipose Nuclei	Adipose
11	chr15:43333600-43363200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:43333600-43367400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr15:43333600-43367400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr15:43333600-43367600	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:43333600-43367600	Strong transcription	Monocytes-CD14+_RO01746	blood
16	chr15:43333600-43367800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr15:43333600-43367800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr15:43333600-43377200	Weak transcription	Stomach Mucosa	stomach
19	chr15:43334000-43367400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:43337800-43358200	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr15:43340200-43380000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr15:43343600-43367400	Strong transcription	Primary neutrophils fromperipheralblood	blood
23	chr15:43344600-43365600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:43345400-43393400	Weak transcription	Psoas Muscle	Psoas
25	chr15:43345600-43361800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:43346600-43362400	Weak transcription	Pancreas	Pancrea
27	chr15:43346600-43372600	Weak transcription	Right Ventricle	heart
28	chr15:43346800-43395400	Weak transcription	Small Intestine	intestine
29	chr15:43348000-43364400	Weak transcription	Aorta	Aorta
30	chr15:43348200-43372800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr15:43348200-43378600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr15:43348200-43389600	Weak transcription	Spleen	Spleen
33	chr15:43348400-43364000	Weak transcription	Lung	lung
34	chr15:43348400-43370200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:43348400-43397400	Weak transcription	H9 Cell Line	embryonic stem cell
36	chr15:43348600-43359000	Weak transcription	NHLF	lung
37	chr15:43349400-43363600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:43350000-43361800	Weak transcription	Fetal Heart	heart
39	chr15:43351000-43367400	Strong transcription	Primary T cells from cord blood	blood
40	chr15:43351000-43378800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr15:43351200-43362000	Weak transcription	Brain Substantia Nigra	brain
42	chr15:43351200-43367000	Strong transcription	Fetal Muscle Leg	muscle
43	chr15:43351400-43358800	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:43351400-43361800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
45	chr15:43351600-43358600	Weak transcription	Fetal Kidney	kidney
46	chr15:43351600-43361400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:43351800-43362600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr15:43351800-43373000	Weak transcription	Brain Angular Gyrus	brain
49	chr15:43352400-43358800	Weak transcription	NHEK	skin
50	chr15:43352400-43359200	Weak transcription	Rectal Mucosa Donor 31	rectum

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