Variant report

Variant	rs2798289
Chromosome Location	chr4:3047537-3047538
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	chr4:3046626..3049120-chr4:3114672..3116966,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GRK4-1	chr4:3047154-3047593	NONHSAT094841

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs1263308	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1263309	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313766	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1313767	0.99[ASN][1000 genomes]
rs1313769	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1313770	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1313772	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.98[ASN][1000 genomes]
rs1313773	0.96[ASN][1000 genomes]
rs1313774	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1557213	0.81[CEU][hapmap]
rs1801058	0.81[CEU][hapmap]
rs2067003	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2187695	0.81[CEU][hapmap]
rs2471334	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2471347	0.85[CEU][hapmap];0.80[TSI][hapmap]
rs2798285	0.98[ASN][1000 genomes]
rs2798296	0.91[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.97[ASN][1000 genomes]
rs2798297	0.81[ASN][1000 genomes]
rs2857843	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857846	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2857847	0.99[ASN][1000 genomes]
rs2857849	0.81[CEU][hapmap]
rs2857853	0.93[ASN][1000 genomes]
rs2857936	0.85[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3021126	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	nsv1013440	chr4:2993130-3053503	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2798289	GRK4	cis	cerebellum	SCAN
rs2798289	HTT-AS1	cis	Whole Blood	GTEx

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:3044000-3048600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr4:3044000-3049400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr4:3044200-3049000	Enhancers	Primary T cells fromperipheralblood	blood
4	chr4:3044200-3049400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:3044200-3049400	Weak transcription	HUVEC	blood vessel
6	chr4:3044400-3049200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr4:3044400-3049200	Weak transcription	Stomach Mucosa	stomach
8	chr4:3044400-3050800	Enhancers	Primary B cells from peripheral blood	blood
9	chr4:3044600-3048000	Weak transcription	Right Atrium	heart
10	chr4:3044600-3049200	Weak transcription	Brain Anterior Caudate	brain
11	chr4:3044600-3049200	Weak transcription	Lung	lung
12	chr4:3044600-3049400	Weak transcription	Gastric	stomach
13	chr4:3044800-3050600	Enhancers	Primary B cells from cord blood	blood
14	chr4:3045000-3049200	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:3045000-3049400	Weak transcription	Left Ventricle	heart
16	chr4:3046000-3048000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr4:3046000-3049200	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr4:3046200-3047800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
19	chr4:3046200-3047800	Enhancers	Placenta	Placenta
20	chr4:3046200-3049200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr4:3046400-3047600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr4:3046400-3047800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr4:3046400-3048200	Enhancers	Primary hematopoietic stem cells	blood
24	chr4:3046400-3048200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr4:3046400-3048200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr4:3046400-3048400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr4:3046400-3048400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr4:3046600-3048000	Enhancers	Primary T killer memory cells from peripheral blood	blood
29	chr4:3046600-3048000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr4:3046600-3048200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr4:3046600-3048400	ZNF genes & repeats	GM12878-XiMat	blood
32	chr4:3046600-3049200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr4:3046800-3047600	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
34	chr4:3046800-3047600	Flanking Bivalent TSS/Enh	HepG2	liver
35	chr4:3046800-3048200	Enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr4:3046800-3048200	Enhancers	Thymus	Thymus
37	chr4:3046800-3049200	Weak transcription	Colonic Mucosa	Colon
38	chr4:3047000-3047600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr4:3047000-3047600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr4:3047000-3047800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr4:3047000-3047800	Enhancers	NHDF-Ad	bronchial
42	chr4:3047000-3049200	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr4:3047000-3049200	Weak transcription	Fetal Intestine Small	intestine
44	chr4:3047000-3049200	Weak transcription	Rectal Smooth Muscle	rectum
45	chr4:3047200-3047600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
46	chr4:3047200-3047600	Enhancers	Dnd41	blood
47	chr4:3047200-3047800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
48	chr4:3047200-3049200	Weak transcription	Rectal Mucosa Donor 29	rectum
49	chr4:3047400-3047600	Weak transcription	Primary T cells from cord blood	blood
50	chr4:3047400-3047600	Flanking Active TSS	Osteobl	bone

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