Variant report

Variant	rs942083
Chromosome Location	chr1:47076981-47076982
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47038329..47041159-chr1:47076859..47079950,3	K562	blood:
2	chr1:47076423..47078358-chr1:47078950..47080736,2	K562	blood:
3	chr1:47069986..47078443-chr1:47078833..47084050,15	K562	blood:
4	chr1:47069761..47073093-chr1:47074880..47077549,3	MCF-7	breast:
5	chr1:47076372..47077998-chr1:47081532..47083963,2	MCF-7	breast:
6	chr1:47068458..47072661-chr1:47073535..47079342,7	MCF-7	breast:
7	chr1:47075911..47077658-chr1:47132285..47133898,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction
ENSG00000142961	Chromatin interaction
ENSG00000123472	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10890406	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10890407	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10890408	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211319	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211320	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211323	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211325	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211326	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211327	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12022855	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12136479	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1258010	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258012	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[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];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1258022	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258050	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258051	1.00[CHB][hapmap]
rs1767612	1.00[CHB][hapmap]
rs2297850	0.93[CEU][hapmap];0.80[GIH][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes]
rs35494693	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs36058295	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4275405	1.00[CEU][hapmap]
rs4660357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4660947	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671527	0.89[ASW][hapmap];0.93[CEU][hapmap];0.95[GIH][hapmap];0.82[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6687832	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6704020	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7526249	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7526328	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs946321	1.00[CHB][hapmap]
rs956526	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs956527	1.00[CEU][hapmap];0.85[GIH][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.93[AMR][1000 genomes];0.95[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	nsv1001455	chr1:46828004-47326539	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv534950	chr1:46828004-47326539	Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv1009193	chr1:46939999-47085667	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv870392	chr1:47040676-47095097	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs942083	MMACHC	cis	cerebellum	SCAN
rs942083	C1orf84	cis	cerebellum	SCAN
rs942083	FAM183A	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47070000-47077600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:47070000-47078800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:47070400-47081200	Weak transcription	Fetal Brain Male	brain
4	chr1:47070600-47077200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr1:47070600-47077400	Weak transcription	NH-A	brain
6	chr1:47070600-47077600	Weak transcription	Fetal Heart	heart
7	chr1:47070600-47078400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr1:47070800-47077200	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr1:47070800-47077400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:47070800-47077400	Weak transcription	A549	lung
11	chr1:47071000-47078400	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr1:47071200-47077200	Weak transcription	K562	blood
13	chr1:47071600-47077200	Strong transcription	Fetal Stomach	stomach
14	chr1:47071800-47079200	Weak transcription	Dnd41	blood
15	chr1:47072000-47077000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr1:47072000-47077600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:47072000-47079000	Strong transcription	Fetal Intestine Small	intestine
18	chr1:47072400-47077000	Strong transcription	Lung	lung
19	chr1:47072400-47077000	Strong transcription	Monocytes-CD14+_RO01746	blood
20	chr1:47073000-47077400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr1:47073200-47077000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr1:47073200-47077000	Strong transcription	GM12878-XiMat	blood
23	chr1:47073200-47077200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr1:47073400-47077000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:47073400-47077200	Strong transcription	Primary monocytes fromperipheralblood	blood
26	chr1:47073400-47077200	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:47073400-47079000	Strong transcription	Fetal Intestine Large	intestine
28	chr1:47073600-47077000	Strong transcription	Liver	Liver
29	chr1:47073600-47077200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr1:47073600-47077200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:47073600-47077800	Strong transcription	Primary T cells from cord blood	blood
32	chr1:47073600-47078200	Strong transcription	Primary neutrophils fromperipheralblood	blood
33	chr1:47073800-47077000	Strong transcription	Ovary	ovary
34	chr1:47073800-47077000	Genic enhancers	Pancreas	Pancrea
35	chr1:47074000-47077000	Strong transcription	Primary B cells from cord blood	blood
36	chr1:47074000-47077000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr1:47074000-47077000	Strong transcription	Duodenum Mucosa	Duodenum
38	chr1:47074000-47078800	Strong transcription	NHLF	lung
39	chr1:47074200-47077000	Strong transcription	Fetal Muscle Trunk	muscle
40	chr1:47074200-47077000	Weak transcription	Psoas Muscle	Psoas
41	chr1:47074200-47077400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:47074200-47077400	Weak transcription	Right Atrium	heart
43	chr1:47074200-47079000	Weak transcription	Brain Germinal Matrix	brain
44	chr1:47074400-47077200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr1:47074600-47077000	Strong transcription	Fetal Muscle Leg	muscle
46	chr1:47074800-47077000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr1:47075000-47077000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr1:47075000-47077000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
49	chr1:47075000-47077000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr1:47075000-47079800	Weak transcription	Fetal Kidney	kidney

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