Variant report

Variant	rs1679012
Chromosome Location	chr15:42528676-42528677
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	chr15:42515383..42517801-chr15:42527177..42529552,2	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:65)

rs_ID	r²[population]
rs1062038	0.82[CHB][hapmap]
rs10775126	0.91[CHB][hapmap]
rs10851409	0.90[CHB][hapmap]
rs11070370	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs11631983	0.91[CHB][hapmap]
rs12441700	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs1359003	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs1359004	0.91[CHB][hapmap]
rs1619030	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1624183	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1659212	0.91[CHB][hapmap]
rs1659213	0.82[CHB][hapmap]
rs1659218	0.82[CHB][hapmap]
rs1659219	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1659222	0.82[CHB][hapmap];0.81[CHD][hapmap]
rs1678985	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1678986	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1678991	0.81[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1678992	0.82[CHB][hapmap]
rs1678993	0.82[CHB][hapmap]
rs1679002	0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1679009	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.85[ASN][1000 genomes]
rs1679010	1.00[CHB][hapmap];0.91[CHD][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1703750	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1703754	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs1703755	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs1712418	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs1712421	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2289295	0.91[CHB][hapmap]
rs2620386	0.82[CHB][hapmap]
rs2918459	0.91[CHB][hapmap]
rs2918460	0.82[CHB][hapmap]
rs2918461	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs3743006	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs4329897	0.91[CHB][hapmap]
rs4923940	0.91[CHB][hapmap]
rs4924645	0.91[CHB][hapmap]
rs4924653	0.91[CHB][hapmap]
rs4924658	0.91[CHB][hapmap]
rs598360	0.83[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs622442	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap];0.85[ASN][1000 genomes]
rs633934	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6493027	0.91[CHB][hapmap]
rs660126	1.00[CHB][hapmap];0.92[JPT][hapmap];0.84[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs677878	1.00[CHB][hapmap];0.91[JPT][hapmap];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs678778	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs681029	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs7086	1.00[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes]
rs7163986	0.91[CHB][hapmap]
rs7166785	0.91[CHB][hapmap]
rs7168709	0.91[CHB][hapmap]
rs7179709	0.82[CHB][hapmap]
rs7181742	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs7183015	0.91[CHB][hapmap]
rs7183546	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs751572	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs8024113	0.91[CHB][hapmap]
rs8024732	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs8031315	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs8033080	0.82[CHB][hapmap]
rs8036046	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs8036596	0.91[CHB][hapmap];0.86[CHD][hapmap]
rs8037020	0.91[CHB][hapmap];0.81[CHD][hapmap]
rs9920921	0.91[CHB][hapmap];0.81[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931223	chr15:41989960-42781757	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	81 gene(s)	inside rSNPs	diseases
2	nsv529687	chr15:42157320-42621682	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
3	nsv1049445	chr15:42239738-42830484	Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
4	nsv542366	chr15:42239738-42830484	Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Flanking 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
5	nsv832985	chr15:42371482-42564966	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1054102	chr15:42493052-42528765	Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	esv1799961	chr15:42522773-42545863	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
8	esv1832380	chr15:42522773-42545863	Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Enhancers	TF binding region Chromatin interactive region miRNA target site	4 gene(s)	inside rSNPs	diseases
9	esv1807328	chr15:42525300-42573278	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1679012	CDAN1	cis	parietal	SCAN
rs1679012	CAPN3	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:42500800-42563200	Weak transcription	Stomach Mucosa	stomach
2	chr15:42501000-42534800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:42501000-42536600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr15:42501000-42536800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:42501000-42538000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:42501200-42532400	Strong transcription	Fetal Muscle Trunk	muscle
7	chr15:42501800-42536800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr15:42502000-42535000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:42502200-42534000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:42502200-42536600	Strong transcription	Primary monocytes fromperipheralblood	blood
11	chr15:42502800-42535200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:42502800-42536400	Strong transcription	Fetal Muscle Leg	muscle
13	chr15:42503200-42544000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:42506800-42532000	Strong transcription	Placenta	Placenta
15	chr15:42508000-42532200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr15:42509400-42535200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr15:42511800-42536800	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr15:42513200-42532200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr15:42513800-42534800	Strong transcription	Liver	Liver
20	chr15:42514000-42534800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:42514000-42535200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:42514200-42532400	Strong transcription	Adipose Nuclei	Adipose
23	chr15:42514200-42535200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:42514200-42535200	Strong transcription	Primary T helper cells fromperipheralblood	blood
25	chr15:42514400-42531800	Strong transcription	Primary T cells from cord blood	blood
26	chr15:42514400-42533600	Strong transcription	Primary T cells fromperipheralblood	blood
27	chr15:42514400-42534800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr15:42514400-42535000	Strong transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:42514400-42535000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:42514400-42536400	Strong transcription	Rectal Mucosa Donor 29	rectum
31	chr15:42514400-42536400	Strong transcription	Rectal Mucosa Donor 31	rectum
32	chr15:42514400-42537200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr15:42514600-42535000	Strong transcription	HUES48 Cell Line	embryonic stem cell
34	chr15:42514800-42532000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr15:42515000-42535400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr15:42515000-42544600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr15:42515200-42534800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:42515400-42535400	Strong transcription	Primary T helper cells PMA-I stimulated	--
39	chr15:42515600-42530400	Strong transcription	NH-A	brain
40	chr15:42515600-42532600	Strong transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:42515600-42535000	Strong transcription	Primary B cells from cord blood	blood
42	chr15:42515800-42532400	Strong transcription	Muscle Satellite Cultured Cells	--
43	chr15:42516000-42535200	Strong transcription	Primary B cells from peripheral blood	blood
44	chr15:42519200-42536400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:42519200-42543800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr15:42519200-42543800	Weak transcription	Gastric	stomach
47	chr15:42519400-42532000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:42519400-42562800	Weak transcription	Fetal Heart	heart
49	chr15:42520200-42530200	Weak transcription	Aorta	Aorta
50	chr15:42520200-42561000	Weak transcription	Pancreatic Islets	Pancreatic Islet

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