Variant report

Variant	rs13078840
Chromosome Location	chr3:143700753-143700754
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1025984	1.00[CEU][hapmap];0.93[GIH][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes]
rs10513234	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.98[MKK][hapmap];0.94[YRI][hapmap]
rs10513235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[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]
rs11914731	0.83[EUR][1000 genomes]
rs13068298	1.00[GIH][hapmap];0.93[MEX][hapmap];0.82[TSI][hapmap]
rs13081286	0.91[CEU][hapmap];0.84[EUR][1000 genomes]
rs13086088	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs1466941	0.96[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.86[JPT][hapmap];0.86[TSI][hapmap]
rs16854772	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16854816	0.94[EUR][1000 genomes]
rs16854819	0.94[EUR][1000 genomes]
rs17602500	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs17667256	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs1867608	0.93[EUR][1000 genomes]
rs1867609	0.93[EUR][1000 genomes]
rs1979910	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.86[GIH][hapmap];0.95[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1992093	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs2011080	0.82[EUR][1000 genomes]
rs2164554	0.94[EUR][1000 genomes]
rs2279856	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs34038325	0.82[ASN][1000 genomes]
rs34372603	0.94[EUR][1000 genomes]
rs34683397	0.95[EUR][1000 genomes]
rs35067746	0.94[EUR][1000 genomes]
rs35085196	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs35193361	0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35309714	0.94[EUR][1000 genomes]
rs35362423	0.82[ASN][1000 genomes]
rs35629416	0.94[EUR][1000 genomes]
rs35649888	0.94[EUR][1000 genomes]
rs35788195	0.95[EUR][1000 genomes]
rs35796781	0.95[EUR][1000 genomes]
rs35877644	0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35959290	0.81[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs4446205	0.81[ASN][1000 genomes]
rs4527375	0.84[EUR][1000 genomes]
rs4561830	0.83[EUR][1000 genomes]
rs4563409	0.81[ASN][1000 genomes]
rs4611822	0.94[EUR][1000 genomes]
rs4613453	0.83[EUR][1000 genomes]
rs4616638	0.83[EUR][1000 genomes]
rs59768870	0.93[EUR][1000 genomes]
rs60367530	0.95[EUR][1000 genomes]
rs60676654	0.94[EUR][1000 genomes]
rs62268458	0.94[EUR][1000 genomes]
rs62269895	0.93[EUR][1000 genomes]
rs6440210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6440212	0.82[EUR][1000 genomes]
rs6766544	0.94[EUR][1000 genomes]
rs6766685	0.94[EUR][1000 genomes]
rs6767236	1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap]
rs6768153	0.95[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6769910	0.94[EUR][1000 genomes]
rs6778627	0.94[EUR][1000 genomes]
rs6779321	0.94[EUR][1000 genomes]
rs6783089	0.94[EUR][1000 genomes]
rs6791078	0.94[EUR][1000 genomes]
rs6795008	0.83[EUR][1000 genomes]
rs6796460	0.82[EUR][1000 genomes]
rs6804060	0.85[GIH][hapmap]
rs721572	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7610378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap]
rs7611326	0.83[EUR][1000 genomes]
rs7634145	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs7637912	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs7639366	0.82[EUR][1000 genomes]
rs7642551	0.83[EUR][1000 genomes]
rs7642774	0.94[EUR][1000 genomes]
rs7646187	0.94[EUR][1000 genomes]
rs7650172	0.83[EUR][1000 genomes]
rs920159	0.93[EUR][1000 genomes]
rs9755502	0.93[EUR][1000 genomes]
rs9755515	0.89[EUR][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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv518814	chr3:143666825-143703750	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13078840	C3orf58	cis	cerebellum	SCAN
rs13078840	HPS3	cis	cerebellum	SCAN

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143692600-143707800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
3	chr3:143693400-143706800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr3:143693400-143708400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr3:143693400-143708400	Weak transcription	Psoas Muscle	Psoas
6	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr3:143693600-143711600	Weak transcription	Left Ventricle	heart
8	chr3:143693800-143701600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr3:143694000-143708000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr3:143694200-143703200	Weak transcription	Placenta	Placenta
11	chr3:143694200-143705600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr3:143694400-143708400	Weak transcription	Fetal Intestine Small	intestine
13	chr3:143694400-143718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr3:143694400-143719400	Weak transcription	Hela-S3	cervix
15	chr3:143694800-143707200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:143695600-143710200	Weak transcription	Fetal Brain Male	brain
17	chr3:143695600-143716800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr3:143696200-143703800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:143696400-143711600	Weak transcription	Fetal Brain Female	brain
20	chr3:143696400-143711800	Weak transcription	Fetal Intestine Large	intestine
21	chr3:143696600-143704400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr3:143696800-143702800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:143696800-143706600	Weak transcription	Ovary	ovary
24	chr3:143697000-143701400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:143697000-143701600	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr3:143697000-143708000	Weak transcription	HUVEC	blood vessel
27	chr3:143697000-143708400	Weak transcription	K562	blood
28	chr3:143697000-143713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr3:143697000-143722800	Weak transcription	Stomach Smooth Muscle	stomach
30	chr3:143697000-143729200	Weak transcription	Aorta	Aorta
31	chr3:143697200-143708400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
32	chr3:143697200-143708400	Weak transcription	HMEC	breast
33	chr3:143697200-143708400	Weak transcription	NHEK	skin
34	chr3:143697200-143710200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
35	chr3:143697200-143712000	Weak transcription	Adipose Nuclei	Adipose
36	chr3:143697200-143723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr3:143697200-143727800	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:143697400-143700800	Enhancers	Brain Hippocampus Middle	brain
39	chr3:143697400-143708400	Weak transcription	Rectal Mucosa Donor 29	rectum
40	chr3:143697600-143701600	Weak transcription	Primary B cells from cord blood	blood
41	chr3:143697800-143701600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr3:143697800-143703200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr3:143697800-143703400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr3:143697800-143703600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
45	chr3:143697800-143704400	Weak transcription	Primary T cells from cord blood	blood
46	chr3:143697800-143707800	Weak transcription	Primary hematopoietic stem cells	blood
47	chr3:143697800-143707800	Weak transcription	Dnd41	blood
48	chr3:143697800-143708000	Weak transcription	Liver	Liver
49	chr3:143698000-143711000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr3:143698200-143702800	Weak transcription	Colon Smooth Muscle	Colon

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