Variant report

Variant	rs1263360
Chromosome Location	chr4:2861430-2861431
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:2858420..2861914-chr4:2865783..2871462,7	K562	blood:
2	chr4:2844708..2848266-chr4:2857886..2861827,4	K562	blood:
3	chr4:2858420..2863571-chr4:2865919..2871146,8	K562	blood:
4	chr4:2844665..2847425-chr4:2860428..2864789,5	MCF-7	breast:
5	chr4:2860130..2862463-chr4:2876073..2878049,2	K562	blood:

Variant related genes	Relation type
ENSG00000087274	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1012365	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs1242228	0.81[JPT][hapmap];0.85[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1263341	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1263343	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1263345	0.86[CHB][hapmap];0.85[JPT][hapmap]
rs1263347	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs1263348	0.83[EUR][1000 genomes]
rs1263349	0.91[CHB][hapmap]
rs1263359	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1419045	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs16843452	0.90[CHB][hapmap];0.89[CHD][hapmap];0.82[ASN][1000 genomes]
rs16843523	0.95[CHB][hapmap];0.89[CHD][hapmap]
rs1877723	0.82[YRI][hapmap]
rs2004973	0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2051560	0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2071695	0.90[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2097081	0.90[CHB][hapmap];0.87[CHD][hapmap];0.85[JPT][hapmap]
rs2185885	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2237004	0.91[CHB][hapmap];0.89[CHD][hapmap];0.80[JPT][hapmap]
rs2239728	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2282772	0.90[CHB][hapmap];0.85[JPT][hapmap]
rs2282774	0.91[CHB][hapmap];0.84[JPT][hapmap]
rs2285084	0.95[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs2798287	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3775067	0.84[LWK][hapmap];1.00[YRI][hapmap]
rs3775068	0.92[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.84[LWK][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3796469	1.00[CHB][hapmap];0.85[JPT][hapmap]
rs4690000	0.81[ASN][1000 genomes]
rs4690001	0.95[CHB][hapmap];0.89[CHD][hapmap];0.81[ASN][1000 genomes]
rs4690004	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4690005	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4961	1.00[CHB][hapmap];0.89[CHD][hapmap];0.85[JPT][hapmap]
rs4964	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs73082333	0.82[ASN][1000 genomes]
rs762847	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv593435	chr4:2770772-2881256	Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv1010533	chr4:2792848-2873441	Enhancers Bivalent/Poised TSS Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv521858	chr4:2846799-2881256	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv524060	chr4:2850142-2881256	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1263360	GRK4	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2846600-2862400	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr4:2846800-2861800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:2846800-2861800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr4:2846800-2862000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr4:2846800-2862600	Weak transcription	Esophagus	oesophagus
6	chr4:2847200-2862200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr4:2847400-2863600	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr4:2852000-2865800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr4:2854800-2862000	Weak transcription	NHEK	skin
10	chr4:2854800-2862800	Weak transcription	Gastric	stomach
11	chr4:2855000-2863000	Genic enhancers	Primary B cells from peripheral blood	blood
12	chr4:2855000-2863400	Weak transcription	Brain Angular Gyrus	brain
13	chr4:2855200-2862400	Genic enhancers	Primary B cells from cord blood	blood
14	chr4:2856200-2862400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr4:2856400-2862600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr4:2856600-2861800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
17	chr4:2856600-2862200	Enhancers	HepG2	liver
18	chr4:2856600-2862800	Weak transcription	Brain Germinal Matrix	brain
19	chr4:2856800-2861800	Weak transcription	Fetal Kidney	kidney
20	chr4:2856800-2862600	Weak transcription	Thymus	Thymus
21	chr4:2856800-2863800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr4:2857000-2861800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr4:2857000-2877000	Weak transcription	Dnd41	blood
24	chr4:2857200-2867600	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr4:2857400-2870000	Enhancers	Primary T helper cells PMA-I stimulated	--
26	chr4:2857400-2877600	Weak transcription	HMEC	breast
27	chr4:2857600-2867400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
28	chr4:2857800-2862800	Weak transcription	Aorta	Aorta
29	chr4:2858200-2864800	Enhancers	Liver	Liver
30	chr4:2858400-2867200	Enhancers	Rectal Mucosa Donor 31	rectum
31	chr4:2858800-2865200	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr4:2859000-2865200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
33	chr4:2859000-2865200	Enhancers	Fetal Muscle Leg	muscle
34	chr4:2859200-2862400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr4:2859200-2862800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr4:2859200-2863400	Enhancers	Skeletal Muscle Male	skeletal muscle
37	chr4:2859200-2869400	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr4:2859400-2865000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr4:2859400-2865000	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr4:2859400-2865400	Enhancers	HSMMtube	muscle
41	chr4:2859400-2865800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr4:2859400-2867200	Enhancers	Small Intestine	intestine
43	chr4:2859600-2861800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr4:2859600-2862600	Weak transcription	Placenta	Placenta
45	chr4:2859600-2864800	Enhancers	HUVEC	blood vessel
46	chr4:2859600-2865600	Enhancers	Adipose Nuclei	Adipose
47	chr4:2859600-2866000	Enhancers	Duodenum Mucosa	Duodenum
48	chr4:2859800-2864000	Enhancers	NHDF-Ad	bronchial
49	chr4:2859800-2864800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
50	chr4:2859800-2865000	Enhancers	Osteobl	bone

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