Variant report

Variant	rs2256086
Chromosome Location	chr4:2959672-2959673
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	chr4:2936900..2939416-chr4:2956780..2960043,4	K562	blood:
2	chr4:2948727..2950755-chr4:2959506..2963214,4	K562	blood:

Variant related genes	Relation type
ENSG00000249673	Chromatin interaction

Extended variants
information (count: 60 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1018789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1024323	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap]
rs1054090	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056094	0.81[CEU][hapmap]
rs1063745	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12500735	0.80[EUR][1000 genomes]
rs12502773	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13120295	0.85[ASN][1000 genomes]
rs13146104	0.81[EUR][1000 genomes]
rs1419044	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs1419046	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs1475975	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475976	1.00[CEU][hapmap];0.83[CHB][hapmap];0.91[JPT][hapmap];0.95[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1475977	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1891710	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.87[MEX][hapmap]
rs1967959	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2022485	0.85[CEU][hapmap]
rs2032463	0.96[CEU][hapmap];0.85[CHB][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2040061	0.81[CEU][hapmap]
rs2051555	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2051556	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2185886	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2251457	0.81[CEU][hapmap]
rs2342295	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.91[TSI][hapmap];0.80[EUR][1000 genomes]
rs2471322	0.81[CEU][hapmap];0.84[TSI][hapmap]
rs2471326	0.81[EUR][1000 genomes]
rs2471327	0.92[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.81[EUR][1000 genomes]
rs2471328	0.81[EUR][1000 genomes]
rs2471337	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2471339	0.81[CEU][hapmap]
rs2471340	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2471350	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2488806	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.81[EUR][1000 genomes]
rs2488809	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2488815	0.92[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2515932	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap]
rs2515933	0.88[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap]
rs2515943	1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap]
rs2515960	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2515961	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2960295	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2960296	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2960298	0.81[CEU][hapmap]
rs2960306	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs2960308	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];0.96[MEX][hapmap];0.84[MKK][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3021140	0.81[CEU][hapmap];0.82[TSI][hapmap]
rs3021145	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3021147	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35897740	0.91[ASN][1000 genomes]
rs57191180	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6834738	0.81[EUR][1000 genomes]
rs729826	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1008436	chr4:2947160-3031195	Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	nsv536998	chr4:2947160-3031195	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv593438	chr4:2948456-3030097	Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
8	nsv1008527	chr4:2957814-3019042	Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2256086	NOP14	cis	cerebellum	SCAN
rs2256086	LOC93622	cis	cerebellum	SCAN
rs2256086	GRK4	cis	cerebellum	SCAN
rs2256086	GRK4	cis	Skin Sun Exposed Lower leg	GTEx
rs2256086	GRK4	Cis_1M	lymphoblastoid	RTeQTL
rs2256086	RNF4	cis	cerebellum	SCAN
rs2256086	GRK4	cis	Adipose Subcutaneous	GTEx
rs2256086	GRK4	cis	Whole Blood	GTEx
rs2256086	GRK4	cis	lung	GTEx
rs2256086	GRK4	cis	Thyroid	GTEx
rs2256086	GRK4	cis	Artery Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:2938000-2960400	Weak transcription	Right Atrium	heart
2	chr4:2938200-2962200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr4:2938400-2962200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr4:2938600-2960400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr4:2938600-2960400	Strong transcription	Brain Cingulate Gyrus	brain
6	chr4:2938600-2961000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr4:2938600-2961600	Strong transcription	Primary T cells from cord blood	blood
8	chr4:2938600-2961600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr4:2938800-2961000	Strong transcription	Primary monocytes fromperipheralblood	blood
10	chr4:2938800-2961000	Strong transcription	Primary hematopoietic stem cells	blood
11	chr4:2938800-2961000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr4:2939000-2960200	Strong transcription	Lung	lung
13	chr4:2939000-2961600	Strong transcription	Fetal Stomach	stomach
14	chr4:2939200-2960000	Strong transcription	Stomach Smooth Muscle	stomach
15	chr4:2939200-2960600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr4:2939200-2961000	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:2939200-2963200	Weak transcription	Fetal Heart	heart
18	chr4:2939400-2959800	Strong transcription	Fetal Muscle Leg	muscle
19	chr4:2939400-2960000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr4:2939400-2960400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr4:2939400-2960400	Strong transcription	NHLF	lung
22	chr4:2939400-2960600	Strong transcription	Brain Hippocampus Middle	brain
23	chr4:2939400-2962200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
24	chr4:2939600-2960000	Strong transcription	Spleen	Spleen
25	chr4:2939600-2960800	Strong transcription	Fetal Brain Female	brain
26	chr4:2939600-2961400	Strong transcription	Dnd41	blood
27	chr4:2939600-2961600	Strong transcription	Fetal Thymus	thymus
28	chr4:2939800-2960600	Strong transcription	Brain Inferior Temporal Lobe	brain
29	chr4:2939800-2960600	Strong transcription	HepG2	liver
30	chr4:2940000-2960000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:2940000-2960400	Strong transcription	NHEK	skin
32	chr4:2940000-2962200	Strong transcription	Primary B cells from peripheral blood	blood
33	chr4:2940600-2959800	Strong transcription	Rectal Smooth Muscle	rectum
34	chr4:2941400-2960000	Strong transcription	Brain Angular Gyrus	brain
35	chr4:2941600-2960400	Strong transcription	HMEC	breast
36	chr4:2942600-2960400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr4:2945200-2960600	Strong transcription	Sigmoid Colon	Sigmoid Colon
38	chr4:2945400-2960600	Strong transcription	Rectal Mucosa Donor 31	rectum
39	chr4:2945400-2961600	Strong transcription	Rectal Mucosa Donor 29	rectum
40	chr4:2947200-2960600	Strong transcription	Thymus	Thymus
41	chr4:2948800-2963200	Strong transcription	Fetal Intestine Small	intestine
42	chr4:2949000-2961600	Strong transcription	Duodenum Mucosa	Duodenum
43	chr4:2951000-2960000	Strong transcription	Esophagus	oesophagus
44	chr4:2951800-2960600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:2953200-2960000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr4:2953600-2963200	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr4:2954000-2960200	Strong transcription	Psoas Muscle	Psoas
48	chr4:2954400-2962400	Strong transcription	A549	lung
49	chr4:2954800-2960800	Strong transcription	Hela-S3	cervix
50	chr4:2955200-2959800	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell

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