Variant report

Variant	rs1007686
Chromosome Location	chr1:228651457-228651458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:228651223..228651926-chr1:228675402..228675964,2	K562	blood:
2	chr1:228487466..228489722-chr1:228649770..228652719,2	K562	blood:
3	chr1:228651267..228651991-chr1:228702700..228703388,2	K562	blood:

Variant related genes	Relation type
ENSG00000154358	Chromatin interaction
ENSG00000168159	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10916313	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs10916314	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs10916317	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1150918	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs11581974	0.84[GIH][hapmap]
rs11587839	0.92[EUR][1000 genomes]
rs1188473	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs1188482	0.89[GIH][hapmap]
rs1188483	0.89[GIH][hapmap]
rs1188487	0.89[GIH][hapmap]
rs12094956	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs12131962	0.87[EUR][1000 genomes]
rs12542	0.85[CEU][hapmap]
rs12691493	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs12725863	0.94[EUR][1000 genomes]
rs12735877	1.00[YRI][hapmap]
rs12746910	0.82[EUR][1000 genomes]
rs13373984	0.84[GIH][hapmap];1.00[YRI][hapmap]
rs1886774	0.86[EUR][1000 genomes]
rs1925714	0.85[CEU][hapmap]
rs1925730	0.85[CEU][hapmap]
rs2147959	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2230656	0.84[GIH][hapmap]
rs4653551	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes]
rs4653552	0.93[EUR][1000 genomes]
rs4653960	0.93[EUR][1000 genomes]
rs474600	0.84[GIH][hapmap]
rs503391	0.84[GIH][hapmap]
rs513467	0.84[GIH][hapmap]
rs532465	0.84[GIH][hapmap]
rs564309	0.84[GIH][hapmap]
rs6426503	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659690	0.93[EUR][1000 genomes]
rs6666241	0.93[EUR][1000 genomes]
rs7524236	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs7529055	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7555298	0.87[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs7555386	0.94[EUR][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	esv32853	chr1:227880116-228806209	Enhancers Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	187 gene(s)	inside rSNPs	diseases
2	nsv826908	chr1:227895386-228691100	Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	157 gene(s)	inside rSNPs	diseases
3	nsv523935	chr1:228038124-228681749	Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	137 gene(s)	inside rSNPs	diseases
4	nsv873255	chr1:228254753-228684779	Genic enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS 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 miRNA target site	133 gene(s)	inside rSNPs	diseases
5	nsv873270	chr1:228442663-228699477	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
6	nsv1009891	chr1:228450763-228742676	Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases
7	nsv517545	chr1:228456147-228685999	Enhancers Active TSS Flanking Active TSS Weak transcription 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 miRNA target site	66 gene(s)	inside rSNPs	diseases
8	nsv1013500	chr1:228459134-228849601	Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
9	nsv873279	chr1:228494790-228681195	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
10	nsv873281	chr1:228505739-228656780	Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
11	esv1808261	chr1:228509427-228674518	Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
12	esv2829948	chr1:228509427-228687948	Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
13	nsv549296	chr1:228585837-228720480	Flanking Active TSS Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	64 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1007686	WDR26	cis	cerebellum	SCAN
rs1007686	DUSP5P	cis	cerebellum	SCAN

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:228647600-228651600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:228650800-228651600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
3	chr1:228650800-228651600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
4	chr1:228650800-228651800	Flanking Active TSS	GM12878-XiMat	blood
5	chr1:228650800-228652000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:228650800-228652000	Flanking Active TSS	K562	blood
7	chr1:228651000-228651800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
8	chr1:228651000-228651800	Bivalent Enhancer	Primary hematopoietic stem cells	blood
9	chr1:228651000-228652000	Flanking Active TSS	A549	lung
10	chr1:228651000-228652400	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr1:228651000-228653000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
12	chr1:228651000-228653200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:228651200-228651600	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
14	chr1:228651200-228651600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr1:228651200-228651600	Flanking Bivalent TSS/Enh	Brain Germinal Matrix	brain
16	chr1:228651200-228651600	Bivalent/Poised TSS	Thymus	Thymus
17	chr1:228651200-228651800	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
18	chr1:228651200-228652000	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
19	chr1:228651200-228652000	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
20	chr1:228651200-228652000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
21	chr1:228651200-228652000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
22	chr1:228651200-228652000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:228651200-228652000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
24	chr1:228651200-228652000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr1:228651200-228652000	Flanking Active TSS	Fetal Brain Female	brain
26	chr1:228651200-228652200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr1:228651200-228652200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr1:228651200-228652200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr1:228651200-228652400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr1:228651200-228652800	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
31	chr1:228651200-228652800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
32	chr1:228651200-228653000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:228651200-228653000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
34	chr1:228651200-228653000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
35	chr1:228651200-228653000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
36	chr1:228651200-228653000	Bivalent/Poised TSS	NHLF	lung
37	chr1:228651200-228653200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
38	chr1:228651200-228653200	Bivalent/Poised TSS	Fetal Kidney	kidney
39	chr1:228651200-228653400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr1:228651400-228651600	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr1:228651400-228651600	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr1:228651400-228651600	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr1:228651400-228651600	Bivalent Enhancer	Breast Myoepithelial Primary Cells	Breast
44	chr1:228651400-228651600	Bivalent Enhancer	Primary T cells from cord blood	blood
45	chr1:228651400-228651600	Bivalent Enhancer	Liver	Liver
46	chr1:228651400-228651600	Bivalent Enhancer	Fetal Intestine Small	intestine
47	chr1:228651400-228651600	Bivalent Enhancer	Fetal Lung	lung
48	chr1:228651400-228651600	Bivalent Enhancer	Fetal Muscle Leg	muscle
49	chr1:228651400-228651600	Flanking Bivalent TSS/Enh	Lung	lung
50	chr1:228651400-228651600	Bivalent Enhancer	Skeletal Muscle Female	skeletal muscle

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