Variant report

Variant	rs1982966
Chromosome Location	chr4:143324094-143324095
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1158692	0.85[CEU][hapmap];0.90[JPT][hapmap];0.84[TSI][hapmap]
rs11722756	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511267	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13128245	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13135641	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13138212	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs13140802	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13144939	1.00[ASW][hapmap];0.85[CEU][hapmap];0.90[JPT][hapmap]
rs1391098	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs1489577	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1489578	1.00[ASW][hapmap];0.92[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap];0.94[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1497389	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1497397	0.84[CEU][hapmap];0.81[GIH][hapmap];0.81[JPT][hapmap];0.81[TSI][hapmap]
rs1497398	0.83[CHB][hapmap];0.89[JPT][hapmap]
rs1565306	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17715707	1.00[ASW][hapmap]
rs1812174	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2173209	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2306913	0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2635424	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs2646085	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs2646091	0.90[JPT][hapmap]
rs34830426	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35151914	0.87[ASN][1000 genomes]
rs3775703	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775705	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775706	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775710	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775711	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3775718	1.00[ASW][hapmap]
rs3775720	1.00[ASW][hapmap];0.85[MKK][hapmap]
rs3822157	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6825345	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs716762	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs724131	0.85[CEU][hapmap];0.84[CHB][hapmap];0.90[JPT][hapmap]
rs72724560	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7699598	0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs881611	0.92[CEU][hapmap];0.92[CHB][hapmap];0.92[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931419	0.92[CEU][hapmap];0.90[JPT][hapmap]
rs983767	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
2	nsv830100	chr4:143216951-143393305	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1982966	GYPB	cis	parietal	SCAN
rs1982966	NDUFC1	cis	parietal	SCAN
rs1982966	LSM6	cis	cerebellum	SCAN
rs1982966	C4orf49	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143300200-143326200	Weak transcription	Aorta	Aorta
2	chr4:143301200-143326200	Weak transcription	Gastric	stomach
3	chr4:143301600-143325400	Weak transcription	Left Ventricle	heart
4	chr4:143313000-143326200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr4:143320600-143324600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
6	chr4:143320600-143326600	Active TSS	Primary T cells fromperipheralblood	blood
7	chr4:143320800-143328000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr4:143321000-143326800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
9	chr4:143321400-143326600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
10	chr4:143321400-143326600	Active TSS	Primary T killer memory cells from peripheral blood	blood
11	chr4:143321600-143324400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:143321600-143324400	Transcr. at gene 5' and 3'	Dnd41	blood
13	chr4:143321800-143324200	Transcr. at gene 5' and 3'	HMEC	breast
14	chr4:143322000-143326400	Active TSS	Fetal Muscle Leg	muscle
15	chr4:143322200-143324400	Enhancers	HUES48 Cell Line	embryonic stem cell
16	chr4:143322200-143326600	Active TSS	Primary T helper naive cells from peripheral blood	blood
17	chr4:143322200-143326600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr4:143322400-143324800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr4:143322400-143326400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr4:143322600-143325400	Enhancers	Cortex derived primary cultured neurospheres	brain
21	chr4:143322600-143326600	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr4:143322800-143324400	Flanking Active TSS	Primary T cells from cord blood	blood
23	chr4:143322800-143324400	Flanking Active TSS	NHDF-Ad	bronchial
24	chr4:143322800-143325400	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:143323000-143324200	Transcr. at gene 5' and 3'	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:143323000-143324400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
27	chr4:143323000-143324400	Enhancers	Fetal Lung	lung
28	chr4:143323000-143325400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr4:143323200-143324200	Active TSS	Fetal Muscle Trunk	muscle
30	chr4:143323200-143324200	Enhancers	A549	lung
31	chr4:143323200-143324200	Transcr. at gene 5' and 3'	NHEK	skin
32	chr4:143323200-143324400	Active TSS	Brain Inferior Temporal Lobe	brain
33	chr4:143323200-143324400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr4:143323200-143324400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr4:143323200-143324400	Transcr. at gene 5' and 3'	HSMM	muscle
36	chr4:143323200-143324400	Flanking Active TSS	Osteobl	bone
37	chr4:143323200-143325000	Enhancers	HUES64 Cell Line	embryonic stem cell
38	chr4:143323200-143325000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
39	chr4:143323200-143325400	Enhancers	ES-I3 Cell Line	embryonic stem cell
40	chr4:143323200-143325600	Enhancers	Fetal Heart	heart
41	chr4:143323200-143326600	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr4:143323400-143324200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr4:143323400-143324200	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr4:143323400-143324200	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr4:143323400-143324200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:143323400-143324400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr4:143323400-143325200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
48	chr4:143323400-143325200	Weak transcription	Spleen	Spleen
49	chr4:143323400-143327200	Weak transcription	Small Intestine	intestine
50	chr4:143323600-143324400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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