Variant report

Variant	rs12029322
Chromosome Location	chr1:45970446-45970447
allele	C/T
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	POLR2A	chr1:45969273-45979784	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:45970173..45973097-chr1:46047655..46049258,2	K562	blood:
2	chr1:45963437..45971807-chr1:46047572..46053150,22	K562	blood:
3	chr1:45969759..45971962-chr1:45973196..45977740,5	MCF-7	breast:
4	chr1:45969960..45972308-chr1:45985412..45987180,2	MCF-7	breast:

Variant related genes	Relation type
CCDC163P	TF binding region
MMACHC	TF binding region
ENSG00000132763	Chromatin interaction
ENSG00000132780	Chromatin interaction

Extended variants
information (count: 81 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1006216	0.86[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1007858	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10789463	0.81[JPT][hapmap]
rs10789464	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10890327	0.80[EUR][1000 genomes]
rs10890330	0.90[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211101	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap]
rs11211108	0.81[EUR][1000 genomes]
rs11211111	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.85[JPT][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11211117	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211118	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11211123	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11211128	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12037201	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12042903	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12046816	0.89[CEU][hapmap];0.82[EUR][1000 genomes]
rs12049503	0.80[ASW][hapmap];1.00[CEU][hapmap];0.91[GIH][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];0.85[YRI][hapmap]
rs12066142	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12067642	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12097497	0.83[EUR][1000 genomes]
rs12410493	0.84[EUR][1000 genomes]
rs12564806	0.86[EUR][1000 genomes]
rs1494812	0.89[CEU][hapmap];0.89[CHB][hapmap];0.83[EUR][1000 genomes]
rs1771551	0.81[CEU][hapmap];0.84[MEX][hapmap];0.81[EUR][1000 genomes]
rs1826691	0.86[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.90[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];0.90[MEX][hapmap];0.96[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[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	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2883968	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3219463	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs3219472	0.86[CHB][hapmap];0.82[CHD][hapmap]
rs34673142	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3790582	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.90[MEX][hapmap];0.86[TSI][hapmap];0.82[EUR][1000 genomes]
rs3790583	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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];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]
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]
rs4660858	0.86[CEU][hapmap];0.91[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4660863	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]
rs5015340	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs518216	0.81[GIH][hapmap]
rs55642258	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788261	0.83[EUR][1000 genomes]
rs61788281	0.85[EUR][1000 genomes]
rs61788285	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61788336	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61788356	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][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];0.85[MEX][hapmap];0.86[TSI][hapmap]
rs67683090	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs713358	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[YRI][hapmap];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7528573	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7531253	0.86[CEU][hapmap];0.90[CHB][hapmap];0.84[CHD][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.90[TSI][hapmap];0.81[EUR][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];0.85[MEX][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs781230	0.81[EUR][1000 genomes]
rs781232	0.81[CEU][hapmap];0.90[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];0.94[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][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	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9729395	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[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:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12029322	CYP4Z2P	cis	cerebellum	SCAN
rs12029322	MMACHC	cis	lymphoblastoid	seeQTL
rs12029322	Hs.396207	cis	multi-tissue	Pritchard
rs12029322	IPP	cis	multi-tissue	Pritchard
rs12029322	SPATA19	trans	parietal	SCAN
rs12029322	PRDX1	cis	Thyroid	GTEx
rs12029322	ST3GAL3	cis	parietal	SCAN
rs12029322	TESK2	cis	Whole Blood	GTEx
rs12029322	MUTYH	Cis_1M	lymphoblastoid	RTeQTL
rs12029322	MMACHC	cis	multi-tissue	Pritchard
rs12029322	B4GALT2	cis	parietal	SCAN
rs12029322	C2orf49	trans	lymphoblastoid	RTeQTL
rs12029322	IPP	cis	lymphoblastoid	seeQTL
rs12029322	MAST2	cis	cerebellum	SCAN
rs12029322	IPP	cis	Lymphoblastoid	GTEx
rs12029322	GPBP1L1	cis	Lymphoblastoid	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:45956800-45974000	Weak transcription	Small Intestine	intestine
2	chr1:45966400-45971800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr1:45966400-45973000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr1:45966400-45973000	Weak transcription	Lung	lung
5	chr1:45966400-45975600	Weak transcription	HSMMtube	muscle
6	chr1:45966400-45975800	Weak transcription	Aorta	Aorta
7	chr1:45966600-45973000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:45966600-45984600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr1:45966800-45972800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr1:45966800-45973200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr1:45966800-45973200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr1:45966800-45973600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr1:45966800-45973600	Weak transcription	NHLF	lung
14	chr1:45966800-45973800	Weak transcription	Brain Germinal Matrix	brain
15	chr1:45966800-45974200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:45966800-45975800	Weak transcription	HSMM	muscle
17	chr1:45966800-45975800	Weak transcription	NHDF-Ad	bronchial
18	chr1:45966800-45976000	Weak transcription	Fetal Brain Male	brain
19	chr1:45966800-45976000	Weak transcription	Placenta Amnion	Placenta Amnion
20	chr1:45966800-45980200	Weak transcription	Pancreatic Islets	Pancreatic Islet
21	chr1:45966800-45984800	Weak transcription	Primary neutrophils fromperipheralblood	blood
22	chr1:45967000-45972800	Weak transcription	Right Ventricle	heart
23	chr1:45967000-45973000	Weak transcription	H9 Cell Line	embryonic stem cell
24	chr1:45967000-45973000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:45967000-45973000	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:45967000-45973200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr1:45967000-45973200	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr1:45967000-45973200	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr1:45967000-45973400	Weak transcription	Primary B cells from cord blood	blood
30	chr1:45967000-45973400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr1:45967000-45973800	Weak transcription	Ovary	ovary
32	chr1:45967000-45974000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr1:45967000-45974000	Weak transcription	Colonic Mucosa	Colon
34	chr1:45967000-45974000	Weak transcription	HUVEC	blood vessel
35	chr1:45967000-45974400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr1:45967000-45974400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr1:45967000-45974400	Weak transcription	Osteobl	bone
38	chr1:45967000-45975400	Weak transcription	NH-A	brain
39	chr1:45967000-45975600	Weak transcription	Rectal Smooth Muscle	rectum
40	chr1:45967000-45975800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr1:45967000-45977200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
42	chr1:45967200-45972800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr1:45967200-45972800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr1:45967200-45973000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr1:45967200-45973000	Weak transcription	Primary hematopoietic stem cells	blood
46	chr1:45967200-45973000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr1:45967200-45973000	Weak transcription	Fetal Muscle Leg	muscle
48	chr1:45967200-45973000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr1:45967200-45973200	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr1:45967200-45973200	Weak transcription	Primary T cells fromperipheralblood	blood

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