Variant report

Variant	rs1992093
Chromosome Location	chr3:143689222-143689223
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYC	chr3:143689219-143689255	H1-hESC	embryonic stem cell:	n/a	n/a
2	FOXA1	chr3:143688891-143689242	HepG2	liver:	n/a	n/a
3	POLR2A	chr3:143688647-143691659	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:143688929..143690453-chr9:116724811..116727064,2	MCF-7	breast:

Variant related genes	Relation type
C3orf58	TF binding region

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

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1025984	0.80[CHD][hapmap];0.89[MEX][hapmap]
rs10513234	0.94[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10513235	0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[JPT][hapmap]
rs1125704	0.81[CEU][hapmap]
rs13064130	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs13078840	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs13081286	0.84[CEU][hapmap]
rs1466941	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17602500	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17667256	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.82[AMR][1000 genomes]
rs1979910	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap]
rs2279856	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2885197	0.81[ASN][1000 genomes]
rs34038325	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34071449	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34402874	0.88[ASN][1000 genomes]
rs35072578	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35211123	0.94[ASN][1000 genomes]
rs35362423	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35692092	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35716467	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35877644	0.83[ASN][1000 genomes]
rs4315684	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4446205	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4535221	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4563409	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs59287916	0.88[ASN][1000 genomes]
rs60505453	0.95[ASN][1000 genomes]
rs62267390	0.95[ASN][1000 genomes]
rs6440210	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.81[ASN][1000 genomes]
rs6767811	0.81[CEU][hapmap]
rs6768153	0.94[CHB][hapmap];0.95[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs721572	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs723491	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7610378	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap]
rs7634145	0.84[CEU][hapmap]
rs9683376	0.81[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 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
5	esv3349108	chr3:143676303-143692796	Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1992093	CHST2	cis	parietal	SCAN
rs1992093	C3orf58	cis	cerebellum	SCAN
rs1992093	TM4SF18	cis	cerebellum	SCAN
rs1992093	HPS3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:143680400-143689600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:143683800-143689400	Weak transcription	Brain Substantia Nigra	brain
3	chr3:143684000-143689600	Weak transcription	Pancreas	Pancrea
4	chr3:143685200-143689600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr3:143687600-143689400	Weak transcription	Right Atrium	heart
6	chr3:143688000-143689600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr3:143688800-143689400	Enhancers	Primary hematopoietic stem cells	blood
8	chr3:143688800-143689400	Enhancers	Colon Smooth Muscle	Colon
9	chr3:143688800-143696400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:143689000-143689400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:143689000-143689400	Enhancers	Breast Myoepithelial Primary Cells	Breast
12	chr3:143689000-143689400	Enhancers	Primary monocytes fromperipheralblood	blood
13	chr3:143689000-143689400	Enhancers	Primary B cells from cord blood	blood
14	chr3:143689000-143689400	Enhancers	Cortex derived primary cultured neurospheres	brain
15	chr3:143689000-143689400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr3:143689000-143689400	Enhancers	Brain Cingulate Gyrus	brain
17	chr3:143689000-143689400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr3:143689000-143689400	Enhancers	Fetal Heart	heart
19	chr3:143689000-143689400	Enhancers	Fetal Intestine Small	intestine
20	chr3:143689000-143689400	Enhancers	NHLF	lung
21	chr3:143689000-143689600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
22	chr3:143689000-143693200	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr3:143689000-143694400	Active TSS	ES-I3 Cell Line	embryonic stem cell
24	chr3:143689000-143695400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr3:143689000-143696800	Active TSS	Stomach Smooth Muscle	stomach
26	chr3:143689200-143689400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:143689200-143689400	Enhancers	iPS-15b Cell Line	embryonic stem cell
28	chr3:143689200-143689400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr3:143689200-143689400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr3:143689200-143689400	Enhancers	Primary B cells from peripheral blood	blood
31	chr3:143689200-143689400	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr3:143689200-143689400	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:143689200-143689400	Enhancers	Muscle Satellite Cultured Cells	--
34	chr3:143689200-143689400	Enhancers	Adipose Nuclei	Adipose
35	chr3:143689200-143689400	Enhancers	Brain Angular Gyrus	brain
36	chr3:143689200-143689400	Enhancers	Brain Anterior Caudate	brain
37	chr3:143689200-143689400	Enhancers	Fetal Lung	lung
38	chr3:143689200-143689400	Enhancers	Fetal Stomach	stomach
39	chr3:143689200-143689400	Bivalent Enhancer	Dnd41	blood
40	chr3:143689200-143689400	Enhancers	Hela-S3	cervix
41	chr3:143689200-143689400	Enhancers	HMEC	breast
42	chr3:143689200-143689400	Enhancers	HUVEC	blood vessel
43	chr3:143689200-143689400	Enhancers	NH-A	brain
44	chr3:143689200-143689400	Enhancers	NHEK	skin
45	chr3:143689200-143689600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
46	chr3:143689200-143689600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
47	chr3:143689200-143689600	Enhancers	Primary T killer memory cells from peripheral blood	blood
48	chr3:143689200-143689600	Enhancers	Liver	Liver
49	chr3:143689200-143689600	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
50	chr3:143689200-143689800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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