Variant report

Variant	rs4660357
Chromosome Location	chr1:47067273-47067274
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:47066512..47069474-chr1:47070954..47073416,4	K562	blood:
2	chr1:47053959..47056132-chr1:47066697..47069062,3	K562	blood:
3	chr1:47033343..47035201-chr1:47067108..47069992,2	K562	blood:
4	chr1:47041717..47044206-chr1:47067000..47069818,2	K562	blood:

Variant related genes	Relation type
ENSG00000079277	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10890406	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];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890407	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10890408	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11211319	1.00[CEU][hapmap];0.95[GIH][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211320	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211323	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211324	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211325	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11211326	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11211327	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12022855	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12136479	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1258010	1.00[CHB][hapmap];0.88[CHD][hapmap]
rs1258012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs35494693	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36058295	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4275405	1.00[CEU][hapmap]
rs4660947	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6671527	0.93[CEU][hapmap];0.95[GIH][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6687832	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6704020	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7526249	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7526328	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs942083	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]
rs946321	1.00[CHB][hapmap]
rs956526	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs956527	1.00[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	nsv1015045	chr1:46910546-47067492	Bivalent Enhancer Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv534952	chr1:46910546-47067492	Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
5	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
6	nsv1008246	chr1:47007844-47069845	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
7	nsv1011892	chr1:47010519-47067492	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	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
rs4660357	C1orf84	cis	cerebellum	SCAN
rs4660357	MMACHC	cis	cerebellum	SCAN
rs4660357	FAM183A	cis	cerebellum	SCAN

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:47042600-47069000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr1:47042800-47068800	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr1:47045600-47068800	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr1:47046200-47069000	Weak transcription	Fetal Kidney	kidney
5	chr1:47048400-47069000	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr1:47050600-47068600	Weak transcription	NHDF-Ad	bronchial
7	chr1:47055400-47068800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr1:47056600-47068800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:47057000-47069000	Weak transcription	NH-A	brain
10	chr1:47057600-47069000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:47058000-47068600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr1:47058600-47069200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:47058800-47068600	Weak transcription	Fetal Lung	lung
14	chr1:47058800-47068600	Weak transcription	Hela-S3	cervix
15	chr1:47059000-47068400	Weak transcription	Aorta	Aorta
16	chr1:47059000-47068800	Weak transcription	Ovary	ovary
17	chr1:47059000-47068800	Weak transcription	HUVEC	blood vessel
18	chr1:47059200-47067400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr1:47059200-47068600	Weak transcription	Colonic Mucosa	Colon
20	chr1:47059200-47068600	Weak transcription	Fetal Brain Female	brain
21	chr1:47059200-47068800	Weak transcription	A549	lung
22	chr1:47059600-47068600	Weak transcription	Fetal Muscle Trunk	muscle
23	chr1:47059800-47068600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:47059800-47068600	Weak transcription	Placenta	Placenta
25	chr1:47059800-47068800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr1:47059800-47068800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr1:47059800-47069000	Weak transcription	HSMMtube	muscle
28	chr1:47060000-47068400	Weak transcription	Liver	Liver
29	chr1:47060000-47068600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:47060000-47068600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr1:47060000-47068600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr1:47060000-47068800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
33	chr1:47060000-47068800	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr1:47060000-47068800	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr1:47060000-47069000	Weak transcription	Fetal Intestine Small	intestine
36	chr1:47060000-47069000	Weak transcription	Fetal Stomach	stomach
37	chr1:47060400-47069000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr1:47060800-47068400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr1:47061000-47067400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr1:47061200-47068600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr1:47061200-47068800	Weak transcription	HSMM	muscle
42	chr1:47061400-47068600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr1:47061400-47068600	Weak transcription	Osteobl	bone
44	chr1:47061600-47067400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr1:47061600-47067400	Weak transcription	Dnd41	blood
46	chr1:47061600-47068600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr1:47061600-47068600	Weak transcription	Primary B cells from peripheral blood	blood
48	chr1:47061800-47068400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr1:47062000-47068600	Weak transcription	Primary B cells from cord blood	blood
50	chr1:47063600-47068600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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