Variant report

Variant	rs716762
Chromosome Location	chr4:143272497-143272498
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1158692	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1158693	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12511267	0.83[AMR][1000 genomes]
rs13128245	0.83[AMR][1000 genomes]
rs13138212	0.85[CEU][hapmap];0.91[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes]
rs13144939	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1391098	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1489577	0.92[CEU][hapmap];0.86[GIH][hapmap];0.80[JPT][hapmap];0.91[TSI][hapmap]
rs1489578	0.92[CEU][hapmap];0.84[GIH][hapmap];0.80[JPT][hapmap];0.88[TSI][hapmap]
rs1497389	0.85[CEU][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap]
rs1497397	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1497398	0.96[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1565306	0.84[AMR][1000 genomes]
rs1812174	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1814133	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1982966	0.85[CEU][hapmap];0.90[JPT][hapmap];0.81[TSI][hapmap]
rs2029991	0.97[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2173209	0.82[AMR][1000 genomes]
rs2255497	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2627802	0.86[GIH][hapmap]
rs2627806	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2627837	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2635421	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2635422	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2635424	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2646085	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646086	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2646087	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2646089	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2646090	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2646091	0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs34830426	0.80[AMR][1000 genomes]
rs3775705	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs3822157	0.85[CEU][hapmap];0.80[JPT][hapmap]
rs6825345	0.80[AMR][1000 genomes]
rs724131	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72724560	0.82[AMR][1000 genomes]
rs7699598	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs881611	0.92[CEU][hapmap];0.91[GIH][hapmap];0.80[JPT][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap]
rs882004	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs882005	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs931419	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs980808	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv1027781	chr4:142943485-143306567	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv830099	chr4:143138257-143285055	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs716762	C4orf49	cis	cerebellum	SCAN
rs716762	LSM6	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:143258000-143274800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr4:143258200-143274000	Weak transcription	Dnd41	blood
3	chr4:143264000-143275400	Enhancers	Primary T helper naive cells from peripheral blood	blood
4	chr4:143264600-143274400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr4:143265800-143280600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr4:143266800-143273000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr4:143267200-143273200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr4:143268400-143283200	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr4:143268600-143273800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
10	chr4:143268600-143274000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr4:143268600-143274000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
12	chr4:143269000-143273400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
13	chr4:143269200-143272600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr4:143269400-143278600	Enhancers	Fetal Heart	heart
15	chr4:143270000-143273200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr4:143270000-143274200	Weak transcription	NHEK	skin
17	chr4:143270000-143274600	Weak transcription	Ovary	ovary
18	chr4:143270200-143273200	Weak transcription	NHLF	lung
19	chr4:143270200-143274200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr4:143270200-143274400	Weak transcription	Primary T cells fromperipheralblood	blood
21	chr4:143270200-143275200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr4:143270200-143275200	Weak transcription	Psoas Muscle	Psoas
23	chr4:143270200-143275800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr4:143270400-143274600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr4:143270600-143274000	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr4:143270800-143284000	Enhancers	Primary T killer memory cells from peripheral blood	blood
27	chr4:143271000-143277200	Enhancers	Fetal Lung	lung
28	chr4:143271200-143272600	Weak transcription	Brain Germinal Matrix	brain
29	chr4:143271200-143272800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr4:143271200-143275600	Enhancers	HSMMtube	muscle
31	chr4:143271200-143276800	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr4:143271400-143273000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr4:143271600-143272600	Enhancers	Rectal Mucosa Donor 31	rectum
34	chr4:143271600-143273000	Enhancers	HSMM	muscle
35	chr4:143271600-143273200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr4:143271800-143272600	Enhancers	Stomach Mucosa	stomach
37	chr4:143271800-143272800	Enhancers	HUVEC	blood vessel
38	chr4:143271800-143273200	Enhancers	Brain Hippocampus Middle	brain
39	chr4:143271800-143275400	Enhancers	Cortex derived primary cultured neurospheres	brain
40	chr4:143272000-143272600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr4:143272000-143272600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr4:143272000-143272600	Enhancers	Fetal Intestine Large	intestine
43	chr4:143272000-143272600	Enhancers	Left Ventricle	heart
44	chr4:143272000-143272600	Enhancers	Small Intestine	intestine
45	chr4:143272000-143272600	Enhancers	Stomach Smooth Muscle	stomach
46	chr4:143272000-143272800	Enhancers	Colon Smooth Muscle	Colon
47	chr4:143272000-143272800	Enhancers	Fetal Stomach	stomach
48	chr4:143272000-143273000	Enhancers	Primary hematopoietic stem cells	blood
49	chr4:143272000-143273200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr4:143272000-143273200	Enhancers	NHDF-Ad	bronchial

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