Variant report

Variant	rs4077643
Chromosome Location	chr3:133941898-133941899
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10935104	0.93[CHB][hapmap];0.84[JPT][hapmap];0.88[ASN][1000 genomes]
rs11915143	0.83[EUR][1000 genomes]
rs12635994	0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13068409	0.87[ASN][1000 genomes]
rs13075720	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs13099506	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28514329	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35015318	0.81[ASN][1000 genomes]
rs35111284	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35432681	0.94[EUR][1000 genomes]
rs35775034	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4077158	0.92[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs4280635	0.87[CHB][hapmap];0.87[ASN][1000 genomes]
rs4404422	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439464	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6439469	0.93[ASN][1000 genomes]
rs67022177	0.98[ASN][1000 genomes]
rs6783086	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6783294	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6786384	0.84[ASN][1000 genomes]
rs6795164	0.93[CHB][hapmap];0.92[JPT][hapmap];0.91[ASN][1000 genomes]
rs6796404	0.92[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6804370	0.93[ASN][1000 genomes]
rs73215351	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7429840	0.93[ASN][1000 genomes]
rs7620941	0.80[ASN][1000 genomes]
rs7623609	0.91[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs7639683	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7641162	0.95[ASN][1000 genomes]
rs9809556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9817270	0.81[ASN][1000 genomes]
rs9822076	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9822469	0.87[CHB][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs9822749	0.95[ASN][1000 genomes]
rs9829505	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9839609	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9846664	0.91[ASN][1000 genomes]
rs9846871	0.81[ASN][1000 genomes]
rs9858000	0.91[ASN][1000 genomes]
rs9859680	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];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9860060	0.81[ASN][1000 genomes]
rs9860268	0.81[ASN][1000 genomes]
rs9865773	0.82[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs9865808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9877899	0.81[ASN][1000 genomes]
rs9880098	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9881681	0.81[ASN][1000 genomes]
rs9881896	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9882168	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9882590	0.87[ASN][1000 genomes]
rs9882927	0.87[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	esv3522171	chr3:133889405-134156571	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	esv3522172	chr3:133889405-134156571	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4077643	SOX14	cis	parietal	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
2	chr3:133894800-133946800	Weak transcription	Pancreas	Pancrea
3	chr3:133895000-133950000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr3:133895000-133950200	Weak transcription	Gastric	stomach
5	chr3:133895600-133942800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr3:133909200-133943000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:133919000-133950600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:133919400-133943000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:133920800-133950200	Weak transcription	Aorta	Aorta
10	chr3:133920800-133950200	Weak transcription	Spleen	Spleen
11	chr3:133920800-133950600	Weak transcription	Hela-S3	cervix
12	chr3:133921800-133943000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr3:133928600-133949400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
14	chr3:133930000-133942400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr3:133930000-133950000	Weak transcription	NHDF-Ad	bronchial
16	chr3:133930000-133950400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr3:133930000-133954600	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:133930200-133942600	Weak transcription	Fetal Thymus	thymus
19	chr3:133930200-133942800	Weak transcription	Left Ventricle	heart
20	chr3:133930200-133946400	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr3:133930200-133950000	Weak transcription	HSMM	muscle
22	chr3:133930200-133950200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr3:133930200-133950600	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:133930200-133955000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr3:133930200-133968000	Weak transcription	Fetal Kidney	kidney
26	chr3:133930400-133942400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr3:133930400-133942600	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr3:133930400-133942600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
29	chr3:133930400-133942600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr3:133930400-133942600	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr3:133930400-133942600	Weak transcription	K562	blood
32	chr3:133930400-133943200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr3:133930400-133943400	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr3:133930400-133950200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr3:133930600-133942200	Weak transcription	Primary neutrophils fromperipheralblood	blood
36	chr3:133930600-133957800	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:133931400-133950200	Weak transcription	Dnd41	blood
38	chr3:133932400-133947000	Weak transcription	Brain Anterior Caudate	brain
39	chr3:133932400-133951000	Weak transcription	NHLF	lung
40	chr3:133933600-133942800	Weak transcription	Primary T cells fromperipheralblood	blood
41	chr3:133933600-133942800	Weak transcription	Adipose Nuclei	Adipose
42	chr3:133933600-133950000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr3:133933800-133942600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr3:133934400-133942800	Weak transcription	Fetal Muscle Trunk	muscle
45	chr3:133934600-133950400	Weak transcription	Brain Hippocampus Middle	brain
46	chr3:133935400-133954600	Weak transcription	HUVEC	blood vessel
47	chr3:133936000-133942800	Weak transcription	Cortex derived primary cultured neurospheres	brain
48	chr3:133936000-133943000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr3:133936200-133942600	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr3:133937600-133942000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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