Variant report

Variant	rs1979910
Chromosome Location	chr3:143710268-143710269
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143690286..143692409-chr3:143708074..143710291,2	K562	blood:
2	chr3:143708397..143711277-chr3:143725553..143727081,2	K562	blood:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	C3orf58	hsa-miR-155-5p	chr3:143710262-143710285

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction
C3orf58	miRNA target site

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs1025984	1.00[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes]
rs10513234	0.95[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap]
rs10513235	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]
rs11914731	0.88[EUR][1000 genomes]
rs13068298	0.86[GIH][hapmap]
rs13078840	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]
rs13081286	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs13086088	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs1466941	0.84[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];0.86[TSI][hapmap];0.85[YRI][hapmap]
rs16854772	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16854816	0.99[EUR][1000 genomes]
rs16854819	0.99[EUR][1000 genomes]
rs17602500	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs17667256	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1867608	0.98[EUR][1000 genomes]
rs1867609	0.98[EUR][1000 genomes]
rs1992093	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2011080	0.87[EUR][1000 genomes]
rs2164554	0.97[EUR][1000 genomes]
rs2279856	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs34372603	0.99[EUR][1000 genomes]
rs34683397	0.98[EUR][1000 genomes]
rs35067746	0.99[EUR][1000 genomes]
rs35085196	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35193361	0.98[EUR][1000 genomes]
rs35309714	0.99[EUR][1000 genomes]
rs35629416	0.97[EUR][1000 genomes]
rs35649888	0.99[EUR][1000 genomes]
rs35716467	0.81[ASN][1000 genomes]
rs35788195	0.98[EUR][1000 genomes]
rs35796781	0.98[EUR][1000 genomes]
rs35877644	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35959290	0.98[EUR][1000 genomes]
rs4527375	0.88[EUR][1000 genomes]
rs4561830	0.88[EUR][1000 genomes]
rs4611822	0.99[EUR][1000 genomes]
rs4613453	0.88[EUR][1000 genomes]
rs4616638	0.88[EUR][1000 genomes]
rs59768870	0.98[EUR][1000 genomes]
rs60367530	0.98[EUR][1000 genomes]
rs60676654	0.99[EUR][1000 genomes]
rs62268458	0.97[EUR][1000 genomes]
rs62269895	0.98[EUR][1000 genomes]
rs6440210	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6440212	0.87[EUR][1000 genomes]
rs6766544	0.99[EUR][1000 genomes]
rs6766685	0.99[EUR][1000 genomes]
rs6767236	0.86[GIH][hapmap];0.88[TSI][hapmap]
rs6768153	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6769910	0.99[EUR][1000 genomes]
rs6778627	0.99[EUR][1000 genomes]
rs6779321	0.99[EUR][1000 genomes]
rs6783089	0.99[EUR][1000 genomes]
rs6791078	0.99[EUR][1000 genomes]
rs6795008	0.88[EUR][1000 genomes]
rs6796460	0.87[EUR][1000 genomes]
rs6804060	0.84[GIH][hapmap]
rs721572	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7610378	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap]
rs7611326	0.88[EUR][1000 genomes]
rs7634145	0.91[CEU][hapmap];0.87[EUR][1000 genomes]
rs7637912	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs7639366	0.87[EUR][1000 genomes]
rs7642551	0.88[EUR][1000 genomes]
rs7642774	0.99[EUR][1000 genomes]
rs7646187	0.97[EUR][1000 genomes]
rs7650145	0.83[EUR][1000 genomes]
rs7650172	0.88[EUR][1000 genomes]
rs920159	0.98[EUR][1000 genomes]
rs9755502	0.97[EUR][1000 genomes]
rs9755515	0.94[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1979910	HPS3	cis	cerebellum	SCAN
rs1979910	C3orf58	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143692800-143714200	Weak transcription	Small Intestine	intestine
2	chr3:143693400-143713800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr3:143693600-143711600	Weak transcription	Left Ventricle	heart
4	chr3:143694400-143718800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr3:143694400-143719400	Weak transcription	Hela-S3	cervix
6	chr3:143695600-143716800	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr3:143696400-143711600	Weak transcription	Fetal Brain Female	brain
8	chr3:143696400-143711800	Weak transcription	Fetal Intestine Large	intestine
9	chr3:143697000-143713400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr3:143697000-143722800	Weak transcription	Stomach Smooth Muscle	stomach
11	chr3:143697000-143729200	Weak transcription	Aorta	Aorta
12	chr3:143697200-143712000	Weak transcription	Adipose Nuclei	Adipose
13	chr3:143697200-143723000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr3:143697200-143727800	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr3:143698000-143711000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr3:143698400-143721200	Weak transcription	Fetal Kidney	kidney
17	chr3:143699000-143717000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr3:143699200-143737600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr3:143699400-143712200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr3:143699400-143714000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:143700400-143720400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
22	chr3:143702400-143717000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr3:143702600-143727400	Weak transcription	Pancreas	Pancrea
24	chr3:143703200-143720600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
25	chr3:143703400-143719400	Weak transcription	Placenta	Placenta
26	chr3:143704000-143711400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:143704400-143716200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:143704600-143712400	Weak transcription	Gastric	stomach
29	chr3:143704600-143719600	Weak transcription	Colon Smooth Muscle	Colon
30	chr3:143704600-143725800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
31	chr3:143705600-143722600	Weak transcription	Esophagus	oesophagus
32	chr3:143706000-143715000	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr3:143706400-143712600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr3:143706400-143728000	Weak transcription	Fetal Stomach	stomach
35	chr3:143706600-143714000	Weak transcription	Fetal Muscle Trunk	muscle
36	chr3:143706600-143722600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
37	chr3:143706800-143710600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr3:143706800-143713200	Weak transcription	Thymus	Thymus
39	chr3:143706800-143725000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr3:143707000-143722600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:143707200-143710600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr3:143707400-143710600	Strong transcription	HSMM	muscle
43	chr3:143707400-143714200	Weak transcription	Brain Anterior Caudate	brain
44	chr3:143707400-143714200	Weak transcription	Brain Substantia Nigra	brain
45	chr3:143707400-143714400	Weak transcription	Brain Cingulate Gyrus	brain
46	chr3:143707400-143714600	Weak transcription	Brain Angular Gyrus	brain
47	chr3:143707600-143711200	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr3:143707800-143710400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:143707800-143711600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr3:143707800-143712600	Strong transcription	Primary T helper cells fromperipheralblood	blood

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