Variant report

Variant	rs1216779
Chromosome Location	chr1:113570560-113570561
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:113564257..113567522-chr1:113568390..113572555,4	K562	blood:
2	chr1:113570114..113572755-chr1:113573147..113575592,2	K562	blood:
3	chr1:113556085..113558248-chr1:113569856..113571725,2	K562	blood:
4	chr1:113564641..113566837-chr1:113568390..113571162,2	K562	blood:

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs11102562	0.86[GIH][hapmap]
rs11102573	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11102574	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102575	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102577	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11102578	0.83[EUR][1000 genomes]
rs11102582	0.87[JPT][hapmap]
rs11584099	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11584535	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11588345	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11590170	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590174	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12028967	0.89[GIH][hapmap]
rs12066274	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12128904	0.94[ASN][1000 genomes]
rs12129863	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12140104	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1216766	0.83[EUR][1000 genomes]
rs1216772	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216773	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216775	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1216781	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs1216783	0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216784	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1216785	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1216790	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12184285	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12354228	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12740564	0.89[EUR][1000 genomes]
rs12744009	0.80[CEU][hapmap];0.89[JPT][hapmap]
rs12745675	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12746771	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12754835	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1419136	0.83[EUR][1000 genomes]
rs1539625	0.84[GIH][hapmap]
rs1544227	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1627925	0.95[ASN][1000 genomes]
rs17014850	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17030901	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17030905	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17030974	0.80[CEU][hapmap];0.94[JPT][hapmap]
rs1728218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1728219	0.95[ASN][1000 genomes]
rs1728232	0.94[ASN][1000 genomes]
rs1728238	0.89[JPT][hapmap]
rs1766862	0.80[CEU][hapmap];0.81[CHD][hapmap];0.94[JPT][hapmap]
rs1778024	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs1778025	0.81[CHD][hapmap];0.94[JPT][hapmap]
rs1983929	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2769259	0.90[ASN][1000 genomes]
rs2798687	0.83[EUR][1000 genomes]
rs2798689	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2798691	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2798692	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34233065	0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34565381	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3889656	1.00[CEU][hapmap];0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3951437	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4301628	0.89[GIH][hapmap]
rs4838975	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4839273	0.89[GIH][hapmap]
rs61818171	0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818172	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818173	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818174	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61818176	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6656041	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6656311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71659385	0.85[ASN][1000 genomes]
rs773430	0.88[ASN][1000 genomes]
rs773432	0.88[ASN][1000 genomes]
rs773433	0.88[ASN][1000 genomes]
rs773434	0.86[ASN][1000 genomes]
rs773435	0.87[ASN][1000 genomes]
rs773436	0.90[ASN][1000 genomes]
rs773439	0.89[ASN][1000 genomes]
rs773440	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9429508	0.83[EUR][1000 genomes]
rs9429509	0.81[EUR][1000 genomes]
rs9787311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002971	chr1:112924725-113740584	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
2	nsv535059	chr1:112924725-113740584	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	166 gene(s)	inside rSNPs	diseases
3	nsv1010276	chr1:113123932-113740584	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised 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 miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv533295	chr1:113167645-113589588	Flanking Active TSS Active TSS Strong transcription Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	93 gene(s)	inside rSNPs	diseases
5	nsv1012119	chr1:113214869-113759081	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
6	nsv535060	chr1:113214869-113759081	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
7	nsv529238	chr1:113229946-113759080	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	100 gene(s)	inside rSNPs	diseases
8	nsv997426	chr1:113288282-113639507	Active TSS Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
9	nsv999915	chr1:113360145-113684833	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
10	esv18293	chr1:113375437-113852815	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
11	nsv1007045	chr1:113425222-113839910	Genic enhancers Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer 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	59 gene(s)	inside rSNPs	diseases
12	nsv946146	chr1:113567302-113640814	Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv427719	chr1:113570229-114078388	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1216779	DENND2C	cis	parietal	SCAN
rs1216779	GPR3	trans	parietal	SCAN
rs1216779	SLC6A17	cis	parietal	SCAN
rs1216779	LRIG2	cis	parietal	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:113541000-113573800	Weak transcription	Right Ventricle	heart
2	chr1:113543200-113574400	Weak transcription	HSMM	muscle
3	chr1:113553000-113572200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:113555600-113572200	Weak transcription	Primary T cells from cord blood	blood
5	chr1:113555600-113584200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr1:113562400-113574000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:113564600-113577600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr1:113564600-113577600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr1:113564800-113579400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr1:113564800-113583000	Weak transcription	Stomach Mucosa	stomach
11	chr1:113568800-113570800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr1:113569000-113571400	Enhancers	ES-I3 Cell Line	embryonic stem cell
13	chr1:113569000-113571600	Enhancers	iPS-15b Cell Line	embryonic stem cell
14	chr1:113569000-113571800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr1:113569200-113571600	Enhancers	HUES64 Cell Line	embryonic stem cell
16	chr1:113569200-113572000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr1:113569400-113570600	Enhancers	Skeletal Muscle Female	skeletal muscle
18	chr1:113569400-113571000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:113569600-113570600	Flanking Active TSS	HepG2	liver
20	chr1:113570000-113571600	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr1:113570200-113570800	Weak transcription	Placenta	Placenta
22	chr1:113570200-113571000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:113570200-113571200	Enhancers	iPS-20b Cell Line	embryonic stem cell
24	chr1:113570200-113571400	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr1:113570200-113572400	Weak transcription	Fetal Heart	heart
26	chr1:113570200-113573600	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:113570200-113575000	Enhancers	Liver	Liver
28	chr1:113570400-113572200	Weak transcription	Left Ventricle	heart
29	chr1:113570400-113572200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr1:113570400-113573200	Weak transcription	Fetal Intestine Small	intestine
31	chr1:113570400-113579400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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