Variant report

Variant	rs4633317
Chromosome Location	chr1:45985157-45985158
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45984510..45988941-chr1:46031540..46035902,8	MCF-7	breast:
2	chr1:45973182..45975128-chr1:45984664..45989019,3	MCF-7	breast:
3	chr1:45982342..45989534-chr1:46006947..46020678,57	K562	blood:
4	chr1:45975860..45989626-chr1:46030076..46041078,36	K562	blood:
5	chr1:45976870..45989534-chr1:46007918..46019226,54	K562	blood:
6	chr1:45984465..45989261-chr1:46150683..46156386,7	K562	blood:
7	chr1:45982844..45990993-chr1:46030121..46038313,25	K562	blood:
8	chr1:45980210..45995142-chr1:46046095..46057139,89	K562	blood:
9	chr1:45974558..45995867-chr1:46046173..46057010,94	K562	blood:
10	chr1:45982314..45985214-chr1:46047500..46050905,5	MCF-7	breast:
11	chr1:45978447..45985278-chr1:46015169..46019739,8	MCF-7	breast:
12	chr1:45770153..45772059-chr1:45985117..45987576,2	K562	blood:
13	chr1:45984460..45986056-chr1:46058706..46061606,2	K562	blood:
14	chr1:45982735..45988890-chr1:46031987..46038228,10	MCF-7	breast:
15	chr1:45984572..45987422-chr1:46019368..46021467,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000117448	Chromatin interaction
ENSG00000162415	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000159596	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000159592	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1006216	0.86[CEU][hapmap];0.86[CHB][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1007858	0.82[AMR][1000 genomes]
rs10789464	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10890330	0.90[CEU][hapmap];0.86[CHB][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11211101	0.82[CHB][hapmap]
rs11211111	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11211117	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211118	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11211123	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211124	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11211128	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11211137	0.82[EUR][1000 genomes]
rs11211139	0.83[EUR][1000 genomes]
rs12029322	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12037201	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12042903	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12046816	0.89[CEU][hapmap]
rs12049503	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.87[JPT][hapmap];0.84[LWK][hapmap];0.95[MEX][hapmap];0.85[YRI][hapmap];0.82[EUR][1000 genomes]
rs12066142	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12067642	0.87[EUR][1000 genomes]
rs12077621	0.83[EUR][1000 genomes]
rs12564806	0.85[EUR][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.83[CHB][hapmap]
rs1771551	0.81[CEU][hapmap];0.84[MEX][hapmap]
rs1826691	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap]
rs2055145	0.90[CEU][hapmap];0.86[CHB][hapmap];0.90[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2153609	0.82[CHB][hapmap]
rs2185549	0.82[CHB][hapmap]
rs28555082	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2883968	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3219463	0.82[CHB][hapmap]
rs3219472	0.82[CHB][hapmap]
rs34673142	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34768551	0.83[EUR][1000 genomes]
rs3790582	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs3790583	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3790585	0.85[YRI][hapmap]
rs4660849	0.82[CHB][hapmap]
rs4660851	0.81[CEU][hapmap]
rs4660852	0.82[CHB][hapmap]
rs4660858	0.86[CEU][hapmap];0.86[CHB][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4660863	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5015340	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs518216	0.81[GIH][hapmap]
rs55642258	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61788281	0.81[EUR][1000 genomes]
rs61788285	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61788336	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61788356	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6657284	0.86[CEU][hapmap];0.86[CHB][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs67683090	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs713358	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7528573	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7531253	0.86[CEU][hapmap];0.86[CHB][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap]
rs7544178	0.82[CHB][hapmap]
rs7553318	0.82[CHB][hapmap]
rs781226	0.81[CEU][hapmap];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs781232	0.81[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs868351	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9326141	0.82[CHB][hapmap]
rs9429076	0.81[CEU][hapmap]
rs9429160	0.82[CHB][hapmap]
rs9727262	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9729395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][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	nsv498036	chr1:45428030-46050934	Active TSS Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	esv1795802	chr1:45819489-46009818	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
3	esv1831217	chr1:45819489-46009818	Strong transcription Enhancers Genic enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
4	nsv530016	chr1:45868543-46069020	Flanking Active TSS Genic enhancers Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
5	nsv829726	chr1:45897581-46103186	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	148 gene(s)	inside rSNPs	diseases
6	nsv529631	chr1:45905936-46335246	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	207 gene(s)	inside rSNPs	diseases
7	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
8	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4633317	MMACHC	cis	multi-tissue	Pritchard
rs4633317	C2orf49	trans	lymphoblastoid	RTeQTL
rs4633317	ST3GAL3	cis	parietal	SCAN
rs4633317	MMACHC	cis	lymphoblastoid	seeQTL
rs4633317	MAST2	cis	cerebellum	SCAN
rs4633317	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs4633317	B4GALT2	cis	parietal	SCAN
rs4633317	IPP	cis	lymphoblastoid	seeQTL
rs4633317	PRDX1	cis	Thyroid	GTEx
rs4633317	SPATA19	trans	parietal	SCAN
rs4633317	CYP4Z2P	cis	cerebellum	SCAN
rs4633317	TESK2	cis	Whole Blood	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45981000-45986000	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr1:45982000-45985400	Transcr. at gene 5' and 3'	A549	lung
3	chr1:45983000-45985200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:45983200-45985200	Weak transcription	Right Ventricle	heart
5	chr1:45983200-45986000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr1:45983200-45986000	Weak transcription	Gastric	stomach
7	chr1:45983200-45986400	Weak transcription	Pancreas	Pancrea
8	chr1:45983600-45986000	Enhancers	Fetal Brain Male	brain
9	chr1:45983800-45986000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr1:45984000-45985200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr1:45984000-45985400	Weak transcription	Lung	lung
12	chr1:45984400-45985200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr1:45984400-45985200	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr1:45984400-45985200	Transcr. at gene 5' and 3'	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr1:45984400-45985200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr1:45984400-45985200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:45984400-45985200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:45984400-45985200	Transcr. at gene 5' and 3'	Brain Substantia Nigra	brain
19	chr1:45984400-45985200	Flanking Active TSS	Fetal Brain Female	brain
20	chr1:45984400-45985400	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:45984400-45985400	Transcr. at gene 5' and 3'	HUES6 Cell Line	embryonic stem cell
22	chr1:45984400-45985400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:45984400-45985400	Enhancers	Fetal Heart	heart
24	chr1:45984400-45985600	Transcr. at gene 5' and 3'	iPS-20b Cell Line	embryonic stem cell
25	chr1:45984400-45985600	Flanking Active TSS	GM12878-XiMat	blood
26	chr1:45984400-45985800	Enhancers	Stomach Mucosa	stomach
27	chr1:45984400-45986000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
28	chr1:45984400-45986000	Enhancers	Primary B cells from cord blood	blood
29	chr1:45984400-45986000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr1:45984400-45986000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
31	chr1:45984400-45986000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr1:45984400-45986000	Enhancers	Fetal Lung	lung
33	chr1:45984400-45986000	Enhancers	Skeletal Muscle Male	skeletal muscle
34	chr1:45984400-45986400	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr1:45984600-45985200	Transcr. at gene 5' and 3'	HUES48 Cell Line	embryonic stem cell
36	chr1:45984600-45985200	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
37	chr1:45984600-45985200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr1:45984600-45985200	Enhancers	Rectal Smooth Muscle	rectum
39	chr1:45984600-45985200	Active TSS	Right Atrium	heart
40	chr1:45984600-45985200	Enhancers	Small Intestine	intestine
41	chr1:45984600-45985200	Transcr. at gene 5' and 3'	Dnd41	blood
42	chr1:45984600-45985200	Transcr. at gene 5' and 3'	HMEC	breast
43	chr1:45984600-45985200	Flanking Active TSS	NH-A	brain
44	chr1:45984600-45985200	Transcr. at gene 5' and 3'	NHEK	skin
45	chr1:45984600-45985200	Flanking Active TSS	NHLF	lung
46	chr1:45984600-45985400	Transcr. at gene 5' and 3'	ES-I3 Cell Line	embryonic stem cell
47	chr1:45984600-45985400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr1:45984600-45985400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
49	chr1:45984600-45985400	Enhancers	Primary T cells from cord blood	blood
50	chr1:45984600-45985400	Flanking Active TSS	Primary hematopoietic stem cells	blood

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