Variant report

Variant	rs2749781
Chromosome Location	chr4:3346617-3346618
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:3345074..3347959-chr4:3442893..3444446,2	MCF-7	breast:
2	chr4:3346041..3348825-chr4:3461682..3464499,2	MCF-7	breast:
3	chr4:3344785..3347772-chr4:3481036..3482952,2	MCF-7	breast:
4	chr4:3345570..3349550-chr4:3443309..3446675,3	MCF-7	breast:
5	chr4:3343221..3349626-chr4:3462156..3471133,16	MCF-7	breast:

Variant related genes	Relation type
ENSG00000175920	Chromatin interaction
ENSG00000109758	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10155132	0.91[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10937924	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13104157	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13150241	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2051558	0.82[CHB][hapmap];0.95[JPT][hapmap]
rs2071666	0.80[ASN][1000 genomes]
rs2071671	0.83[CHB][hapmap]
rs2236052	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2239725	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2748447	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2749778	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2749780	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2749782	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2749783	0.95[CEU][hapmap];0.84[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2749785	0.96[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap]
rs2798221	0.85[CHB][hapmap]
rs2857861	0.81[JPT][hapmap]
rs2857982	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3095081	0.81[CHB][hapmap]
rs3129308	0.96[CEU][hapmap];0.81[CHB][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];0.87[EUR][1000 genomes]
rs3129310	0.96[CEU][hapmap];0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs3129327	0.96[CEU][hapmap];0.90[CHB][hapmap];0.83[MEX][hapmap];0.87[AMR][1000 genomes]
rs3129328	0.96[CEU][hapmap];0.84[JPT][hapmap];0.84[EUR][1000 genomes]
rs3129334	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3135145	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[JPT][hapmap];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3135146	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[MEX][hapmap];0.86[TSI][hapmap];1.00[AFR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs60181496	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60208975	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6819202	0.96[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7435601	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[CHD][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs881816	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs881817	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs910568	0.95[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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	nsv998290	chr4:3176454-3355758	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases
4	nsv878456	chr4:3215835-3467519	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS 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 target site	13 gene(s)	inside rSNPs	diseases
5	nsv428106	chr4:3226182-3752322	Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
6	nsv878462	chr4:3311548-3505448	Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1007847	chr4:3317904-3527357	Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
8	nsv537001	chr4:3317904-3527357	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
9	nsv593446	chr4:3342137-3346617	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv593449	chr4:3342954-3346617	Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv3341831	chr4:3344704-3347502	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2749781	DGKQ	cis	parietal	SCAN
rs2749781	RGS12	cis	cerebellum	SCAN

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3301200-3350000	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr4:3314400-3348200	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr4:3320400-3351800	Weak transcription	Aorta	Aorta
4	chr4:3321000-3347000	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr4:3325600-3348000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr4:3326400-3348000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr4:3334000-3370600	Weak transcription	Right Atrium	heart
8	chr4:3339200-3353200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr4:3342000-3348200	Weak transcription	Brain Angular Gyrus	brain
10	chr4:3342200-3348000	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr4:3342600-3348000	Weak transcription	Liver	Liver
12	chr4:3342600-3350200	Weak transcription	Pancreas	Pancrea
13	chr4:3342800-3348000	Weak transcription	Left Ventricle	heart
14	chr4:3342800-3348000	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr4:3342800-3355400	Weak transcription	Esophagus	oesophagus
16	chr4:3343800-3348000	Weak transcription	Placenta	Placenta
17	chr4:3343800-3350200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr4:3344000-3347800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr4:3344000-3347800	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr4:3344000-3352400	Weak transcription	Sigmoid Colon	Sigmoid Colon
21	chr4:3344000-3354600	Weak transcription	Right Ventricle	heart
22	chr4:3344200-3348000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr4:3344200-3348000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr4:3344200-3348000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr4:3344400-3346800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr4:3344400-3347600	Weak transcription	Primary hematopoietic stem cells	blood
27	chr4:3344400-3347800	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr4:3344400-3348000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr4:3344400-3348000	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr4:3344400-3348000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr4:3344400-3348000	Weak transcription	Brain Cingulate Gyrus	brain
32	chr4:3344400-3348000	Weak transcription	Duodenum Mucosa	Duodenum
33	chr4:3344400-3349600	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr4:3344400-3349800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr4:3344400-3350200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr4:3344400-3350200	Weak transcription	Ovary	ovary
37	chr4:3344400-3350200	Weak transcription	Spleen	Spleen
38	chr4:3344400-3356400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr4:3344400-3362400	Weak transcription	HSMMtube	muscle
40	chr4:3344400-3367600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr4:3344600-3346800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr4:3344600-3346800	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr4:3344600-3347000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr4:3344600-3347000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:3344600-3347200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
46	chr4:3344600-3347800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
47	chr4:3344600-3348000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr4:3344600-3348000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr4:3344600-3348000	Weak transcription	Brain Anterior Caudate	brain
50	chr4:3344600-3349600	Weak transcription	iPS-15b Cell Line	embryonic stem cell

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