Variant report

Variant	rs4660863
Chromosome Location	chr1:45955868-45955869
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:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr1:45954972..45958180-chr1:45986651..45988959,5	K562	blood:
2	chr1:45284051..45286963-chr1:45955416..45958247,2	MCF-7	breast:
3	chr1:45284063..45286769-chr1:45955098..45956816,2	K562	blood:
4	chr1:45804942..45806889-chr1:45955165..45957556,2	K562	blood:
5	chr1:45293211..45295000-chr1:45954094..45956498,2	K562	blood:
6	chr1:45283791..45286747-chr1:45955379..45957255,3	MCF-7	breast:
7	chr1:45954905..45960579-chr1:45960652..45966878,10	K562	blood:
8	chr1:45951915..45956979-chr1:46048471..46052743,8	K562	blood:
9	chr1:45804236..45806527-chr1:45955097..45957372,3	MCF-7	breast:
10	chr1:45451104..45453643-chr1:45953899..45956205,2	K562	blood:
11	chr1:45285250..45286919-chr1:45954512..45956558,2	K562	blood:
12	chr1:45934784..45936489-chr1:45953495..45956365,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000070785	Chromatin interaction
ENSG00000132780	Chromatin interaction
ENSG00000132763	Chromatin interaction
ENSG00000117450	Chromatin interaction
ENSG00000132781	Chromatin interaction
ENSG00000132773	Chromatin interaction
ENSG00000202444	Chromatin interaction
ENSG00000236624	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1006216	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1007858	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10789463	0.81[JPT][hapmap]
rs10789464	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10890327	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10890330	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211101	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs11211108	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11211111	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211117	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211118	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11211123	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11211124	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211128	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12029322	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12037201	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12042903	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12046816	0.89[CEU][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12049503	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.85[YRI][hapmap]
rs12066142	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12067642	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12097497	0.83[EUR][1000 genomes]
rs12410493	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564806	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs1771551	0.81[CEU][hapmap];0.90[MEX][hapmap];0.81[EUR][1000 genomes]
rs1826691	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.82[EUR][1000 genomes]
rs2055145	0.90[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2088100	0.83[EUR][1000 genomes]
rs2153609	0.86[CHB][hapmap];0.81[JPT][hapmap]
rs2185549	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs28555082	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2883968	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3219463	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs3219472	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs34673142	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3790582	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3790583	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3790585	0.85[YRI][hapmap]
rs4520450	0.82[CHD][hapmap]
rs4633317	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]
rs4660849	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs4660851	0.81[CEU][hapmap]
rs4660852	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs4660853	0.82[CHD][hapmap]
rs4660855	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660858	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs5015340	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs518216	0.81[GIH][hapmap]
rs55642258	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788261	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788262	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61788281	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61788285	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788336	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61788356	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs61791369	0.81[EUR][1000 genomes]
rs6657284	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap]
rs67683090	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs713358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7528573	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7531253	0.86[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7543428	0.82[CHD][hapmap]
rs7544178	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs7553318	0.86[CHB][hapmap]
rs781226	0.81[CEU][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs781230	0.81[EUR][1000 genomes]
rs781232	0.81[CEU][hapmap];0.95[MEX][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs868351	1.00[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.90[LWK][hapmap];0.89[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9326141	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs9429076	0.81[CEU][hapmap]
rs9429160	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs9727262	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9729395	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs4660863	MAST2	cis	cerebellum	SCAN
rs4660863	Hs.396207	cis	multi-tissue	Pritchard
rs4660863	MMACHC	cis	multi-tissue	Pritchard
rs4660863	IPP	cis	lymphoblastoid	seeQTL
rs4660863	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs4660863	TESK2	cis	Whole Blood	GTEx
rs4660863	C2orf49	trans	lymphoblastoid	RTeQTL
rs4660863	B4GALT2	cis	parietal	SCAN
rs4660863	ST3GAL3	cis	parietal	SCAN
rs4660863	PRDX1	cis	Thyroid	GTEx
rs4660863	CYP4Z2P	cis	cerebellum	SCAN
rs4660863	MMACHC	cis	lymphoblastoid	seeQTL
rs4660863	SPATA19	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45954800-45956400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
2	chr1:45955000-45956000	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
3	chr1:45955000-45956000	Flanking Active TSS	Brain Hippocampus Middle	brain
4	chr1:45955000-45957400	Active TSS	Brain Inferior Temporal Lobe	brain
5	chr1:45955000-45957600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr1:45955200-45956000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
7	chr1:45955200-45956000	Flanking Active TSS	Primary B cells from peripheral blood	blood
8	chr1:45955200-45956200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
9	chr1:45955200-45956800	Active TSS	Breast Myoepithelial Primary Cells	Breast
10	chr1:45955200-45957400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr1:45955200-45957400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr1:45955200-45957400	Active TSS	Brain Cingulate Gyrus	brain
13	chr1:45955200-45957600	Active TSS	HUES48 Cell Line	embryonic stem cell
14	chr1:45955200-45957600	Active TSS	Colonic Mucosa	Colon
15	chr1:45955400-45956000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
16	chr1:45955400-45956000	Flanking Active TSS	Liver	Liver
17	chr1:45955400-45956000	Flanking Active TSS	Brain Anterior Caudate	brain
18	chr1:45955400-45956000	Weak transcription	Spleen	Spleen
19	chr1:45955400-45956200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr1:45955400-45956200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr1:45955400-45956200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr1:45955400-45956200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr1:45955400-45956200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr1:45955400-45956200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr1:45955400-45956200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr1:45955400-45956200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
27	chr1:45955400-45956400	Flanking Active TSS	Primary B cells from cord blood	blood
28	chr1:45955400-45956400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
29	chr1:45955400-45956400	Flanking Active TSS	Stomach Smooth Muscle	stomach
30	chr1:45955400-45956600	Flanking Active TSS	Primary hematopoietic stem cells	blood
31	chr1:45955400-45956800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
32	chr1:45955400-45956800	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr1:45955400-45957000	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr1:45955400-45957200	Active TSS	Primary T killer memory cells from peripheral blood	blood
35	chr1:45955400-45957200	Active TSS	Brain Angular Gyrus	brain
36	chr1:45955400-45957200	Active TSS	Rectal Mucosa Donor 31	rectum
37	chr1:45955400-45957400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
38	chr1:45955400-45957600	Active TSS	Fetal Intestine Large	intestine
39	chr1:45955400-45957600	Active TSS	Fetal Kidney	kidney
40	chr1:45955400-45957600	Active TSS	Ovary	ovary
41	chr1:45955600-45956000	Flanking Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr1:45955600-45956000	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr1:45955600-45956000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
44	chr1:45955600-45956000	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
45	chr1:45955600-45956000	Bivalent/Poised TSS	Fetal Brain Male	brain
46	chr1:45955600-45956000	Flanking Bivalent TSS/Enh	Fetal Heart	heart
47	chr1:45955600-45956000	Flanking Active TSS	Fetal Lung	lung
48	chr1:45955600-45956000	Flanking Bivalent TSS/Enh	Fetal Stomach	stomach
49	chr1:45955600-45956000	Enhancers	Gastric	stomach
50	chr1:45955600-45956000	Flanking Active TSS	Placenta Amnion	Placenta Amnion

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