Variant report

Variant	rs1012365
Chromosome Location	chr4:2917608-2917609
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:2916201..2917764-chr4:2963610..2965346,2	K562	blood:
2	chr4:2908128..2910686-chr4:2915793..2918014,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000087269	Chromatin interaction
ENSG00000087274	Chromatin interaction
ENSG00000125388	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1242228	0.86[CHB][hapmap]
rs1263338	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1263339	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1263340	0.81[ASN][1000 genomes]
rs1263341	0.82[ASN][1000 genomes]
rs1263342	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263343	0.85[ASN][1000 genomes]
rs1263344	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1263345	0.94[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263347	0.94[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1263349	1.00[CEU][hapmap];0.91[CHB][hapmap];0.91[CHD][hapmap];0.88[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1263359	1.00[CHB][hapmap]
rs1263360	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs12642795	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1419045	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16843452	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];0.83[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.83[ASN][1000 genomes]
rs16843523	0.86[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.83[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];0.86[YRI][hapmap];0.87[ASN][1000 genomes]
rs2051560	0.87[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2071695	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2097081	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2185885	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2237004	0.87[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.98[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2239728	0.87[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2282772	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2282773	0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2282774	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2285084	0.87[ASW][hapmap];0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2301374	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2798287	0.81[ASN][1000 genomes]
rs2857866	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs3775068	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap]
rs3796469	0.94[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4690000	0.89[CEU][hapmap];0.85[ASN][1000 genomes]
rs4690001	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.86[TSI][hapmap];0.84[ASN][1000 genomes]
rs4690065	0.90[AFR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4961	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4963	0.94[CEU][hapmap];0.86[JPT][hapmap];0.86[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4964	0.87[ASW][hapmap];0.82[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73082333	0.86[ASN][1000 genomes]
rs73189458	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs762847	0.95[CHB][hapmap];0.89[CHD][hapmap];0.91[JPT][hapmap];0.80[ASN][1000 genomes]
rs7654786	0.80[ASN][1000 genomes]
rs7664801	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3418626	chr4:2741174-3461492	Genic enhancers Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	esv3397632	chr4:2741239-3460583	Enhancers Flanking Active TSS Weak transcription Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv461163	chr4:2906285-3234980	Enhancers Strong transcription Flanking Active TSS Genic enhancers Weak transcription Bivalent/Poised TSS 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	52 gene(s)	inside rSNPs	diseases
4	nsv593437	chr4:2906285-3234980	Genic enhancers Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1012365	DGKQ	cis	parietal	SCAN
rs1012365	HELT	trans	parietal	SCAN
rs1012365	ZNF732	cis	cerebellum	SCAN
rs1012365	ZFYVE28	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2876600-2919200	Strong transcription	Primary B cells from peripheral blood	blood
2	chr4:2877200-2919400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:2883600-2918600	Strong transcription	Fetal Stomach	stomach
4	chr4:2890400-2918000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:2893000-2919400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:2893200-2918800	Strong transcription	Primary monocytes fromperipheralblood	blood
7	chr4:2893200-2918800	Strong transcription	Fetal Muscle Trunk	muscle
8	chr4:2893200-2919200	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr4:2893200-2932600	Strong transcription	Fetal Thymus	thymus
10	chr4:2893400-2918800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr4:2893400-2919000	Strong transcription	Fetal Muscle Leg	muscle
12	chr4:2893800-2918600	Strong transcription	Thymus	Thymus
13	chr4:2893800-2919000	Strong transcription	Duodenum Mucosa	Duodenum
14	chr4:2894000-2923000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr4:2894800-2919800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr4:2895000-2917800	Strong transcription	Dnd41	blood
17	chr4:2895200-2919000	Strong transcription	Rectal Mucosa Donor 29	rectum
18	chr4:2895400-2919000	Strong transcription	HUES48 Cell Line	embryonic stem cell
19	chr4:2895600-2918400	Strong transcription	HUES6 Cell Line	embryonic stem cell
20	chr4:2895600-2919200	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr4:2895600-2919200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr4:2895800-2919000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr4:2895800-2919200	Strong transcription	Duodenum Smooth Muscle	Duodenum
24	chr4:2895800-2919200	Strong transcription	Skeletal Muscle Female	skeletal muscle
25	chr4:2896400-2918000	Strong transcription	HSMMtube	muscle
26	chr4:2896600-2918800	Strong transcription	Adipose Nuclei	Adipose
27	chr4:2896800-2918000	Strong transcription	Spleen	Spleen
28	chr4:2896800-2918800	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr4:2897200-2917800	Strong transcription	NHEK	skin
30	chr4:2899800-2918400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr4:2899800-2919600	Strong transcription	Brain Germinal Matrix	brain
32	chr4:2901200-2934600	Weak transcription	Hela-S3	cervix
33	chr4:2903000-2925400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr4:2903200-2918800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr4:2903200-2919200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr4:2903200-2919200	Strong transcription	Muscle Satellite Cultured Cells	--
37	chr4:2904000-2918600	Strong transcription	Fetal Intestine Large	intestine
38	chr4:2904000-2919000	Strong transcription	Rectal Smooth Muscle	rectum
39	chr4:2904200-2918600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr4:2904200-2918800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr4:2904400-2918600	Strong transcription	Fetal Intestine Small	intestine
42	chr4:2904600-2919200	Strong transcription	Fetal Brain Female	brain
43	chr4:2904800-2918600	Strong transcription	Ovary	ovary
44	chr4:2904800-2918800	Strong transcription	Stomach Smooth Muscle	stomach
45	chr4:2904800-2919600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr4:2905000-2917800	Strong transcription	NHLF	lung
47	chr4:2905000-2918800	Strong transcription	Skeletal Muscle Male	skeletal muscle
48	chr4:2905000-2919000	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr4:2905000-2919200	Strong transcription	Brain Cingulate Gyrus	brain
50	chr4:2905000-2919200	Strong transcription	Osteobl	bone

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