Variant report

Variant	rs1993813
Chromosome Location	chr15:43273251-43273252
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs1037990	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10467975	1.00[CEU][hapmap];0.92[JPT][hapmap]
rs11070380	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs11070382	1.00[CEU][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.89[EUR][1000 genomes]
rs11070386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11070387	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070388	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11070391	1.00[CEU][hapmap]
rs11630595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11853250	0.88[CEU][hapmap];0.92[JPT][hapmap]
rs12050596	0.91[EUR][1000 genomes]
rs12899266	1.00[CEU][hapmap]
rs12905967	0.83[EUR][1000 genomes]
rs12913617	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1381856	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1462856	1.00[CEU][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.87[EUR][1000 genomes]
rs16957165	1.00[CEU][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap]
rs16957167	1.00[CEU][hapmap]
rs16957244	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs16957250	1.00[CEU][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes]
rs16957264	0.88[CEU][hapmap];0.92[JPT][hapmap];0.94[MEX][hapmap]
rs16957385	0.85[EUR][1000 genomes]
rs1972447	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1996675	0.86[EUR][1000 genomes]
rs2035170	0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2037392	0.80[CEU][hapmap]
rs2054389	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2126602	0.91[EUR][1000 genomes]
rs2412746	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2412747	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2412752	1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap]
rs2682073	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2733224	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28585036	1.00[CEU][hapmap]
rs2899069	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3736054	0.81[CHD][hapmap];0.86[JPT][hapmap];0.88[MEX][hapmap];0.95[TSI][hapmap]
rs3784265	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3803341	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244590	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4338775	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4509988	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4573908	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4923955	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4924701	0.96[EUR][1000 genomes]
rs4924704	1.00[CEU][hapmap];0.81[CHD][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs55805543	0.88[EUR][1000 genomes]
rs60763334	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6416436	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6493071	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6493076	1.00[CEU][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.91[EUR][1000 genomes]
rs6493077	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66530524	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7162939	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7162959	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7174028	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7174915	1.00[CEU][hapmap]
rs7176116	0.84[EUR][1000 genomes]
rs7178567	1.00[CEU][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8027371	0.80[CEU][hapmap]
rs8027733	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8031767	1.00[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8035894	0.82[EUR][1000 genomes]
rs8036710	0.86[EUR][1000 genomes]
rs8037022	0.89[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8042481	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9796571	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9920498	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9920904	0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 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	nsv904134	chr15:43097652-43357406	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	nsv1036512	chr15:43164906-43274531	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	esv3421859	chr15:43249285-43280570	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1993813	CCNDBP1	Cis_1M	lymphoblastoid	RTeQTL
rs1993813	CCNDBP1	cis	multi-tissue	Pritchard
rs1993813	TTBK2	cis	parietal	SCAN
rs1993813	CCNDBP1	cis	Lymphoblastoid	GTEx

Chromatin state (count:124 , 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	chr15:43244000-43276400	Weak transcription	Psoas Muscle	Psoas
3	chr15:43248000-43320600	Weak transcription	Stomach Mucosa	stomach
4	chr15:43249600-43283200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr15:43252400-43298400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:43252800-43295800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
7	chr15:43255200-43278800	Weak transcription	Esophagus	oesophagus
8	chr15:43258800-43277600	Weak transcription	Colonic Mucosa	Colon
9	chr15:43261000-43277000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr15:43262400-43276800	Strong transcription	Primary B cells from peripheral blood	blood
11	chr15:43262600-43292000	Strong transcription	Fetal Muscle Trunk	muscle
12	chr15:43263400-43284000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:43264000-43283000	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr15:43265400-43275400	Strong transcription	NH-A	brain
15	chr15:43265800-43275600	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:43265800-43277200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr15:43265800-43278800	Weak transcription	NHLF	lung
18	chr15:43265800-43283600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:43265800-43296800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:43266000-43292200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:43266400-43294800	Weak transcription	Pancreas	Pancrea
22	chr15:43266800-43286800	Weak transcription	A549	lung
23	chr15:43267000-43276400	Weak transcription	Brain Substantia Nigra	brain
24	chr15:43267200-43278600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:43267200-43278800	Weak transcription	Gastric	stomach
26	chr15:43267200-43278800	Weak transcription	Spleen	Spleen
27	chr15:43267200-43323000	Weak transcription	Pancreatic Islets	Pancreatic Islet
28	chr15:43268200-43274000	Weak transcription	NHEK	skin
29	chr15:43268200-43278800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr15:43268600-43273600	Weak transcription	Colon Smooth Muscle	Colon
31	chr15:43268800-43274800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:43269000-43274600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:43269000-43277600	Weak transcription	Right Ventricle	heart
34	chr15:43269000-43296800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:43269000-43298400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
36	chr15:43269000-43312800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
37	chr15:43269200-43275000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:43269200-43397200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:43269400-43278800	Weak transcription	Placenta Amnion	Placenta Amnion
40	chr15:43269600-43274200	Weak transcription	Brain Cingulate Gyrus	brain
41	chr15:43269600-43275200	Weak transcription	Ovary	ovary
42	chr15:43269600-43276000	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:43269600-43278400	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr15:43269600-43278600	Weak transcription	Brain Germinal Matrix	brain
45	chr15:43269600-43279000	Weak transcription	Aorta	Aorta
46	chr15:43269600-43300200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:43269800-43274200	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr15:43269800-43274200	Weak transcription	NHDF-Ad	bronchial
49	chr15:43269800-43274400	Weak transcription	Fetal Brain Female	brain
50	chr15:43269800-43274600	Weak transcription	Brain Angular Gyrus	brain

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