Variant report

Variant	rs12490149
Chromosome Location	chr3:160939120-160939121
allele	A/G
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	RFX5	chr3:160938543-160939291	Hela-S3	cervix:	n/a	n/a
2	YY1	chr3:160938770-160939580	GM12891	blood:	n/a	chr3:160939248-160939262
3	ZBTB33	chr3:160938866-160939245	HCT-116	colon:	n/a	chr3:160938867-160938874 chr3:160939083-160939098
4	RCOR1	chr3:160938751-160939256	K562	blood:	n/a	n/a
5	POLR2A	chr3:160938734-160939573	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr3:160938855-160939435	ECC-1	luminal epithelium:	n/a	chr3:160939248-160939262
7	FOXP2	chr3:160939101-160939471	PFSK-1	brain:	n/a	n/a
8	CREB1	chr3:160938852-160939224	A549	lung:	n/a	n/a
9	MAX	chr3:160938327-160939653	MCF-7	breast:	n/a	n/a
10	RFX5	chr3:160938707-160939291	HepG2	liver:	n/a	n/a
11	ATF3	chr3:160939091-160939423	HepG2	liver:	n/a	n/a
12	ZEB1	chr3:160938979-160939421	GM12878	blood:	n/a	n/a
13	YY1	chr3:160938772-160939449	GM12878	blood:	n/a	chr3:160939248-160939262
14	HMGN3	chr3:160938907-160939610	K562	blood:	n/a	n/a
15	MAFK	chr3:160938801-160939168	K562	blood:	n/a	n/a
16	POLR2A	chr3:160938673-160939468	GM12892	blood:	n/a	n/a
17	FOXA1	chr3:160938786-160939189	T-47D	breast:	n/a	n/a
18	JUND	chr3:160938910-160939210	HepG2	liver:	n/a	n/a
19	PAX5	chr3:160938842-160939532	GM12878	blood:	n/a	n/a
20	ZBTB33	chr3:160938804-160939261	GM12878	blood:	n/a	chr3:160938867-160938874 chr3:160939083-160939098
21	MAX	chr3:160938831-160939625	K562	blood:	n/a	n/a
22	TCF12	chr3:160938802-160939330	GM12878	blood:	n/a	n/a
23	JUND	chr3:160938834-160939216	HepG2	liver:	n/a	chr3:160938885-160938899
24	MXI1	chr3:160938485-160940211	IMR90	lung:	n/a	n/a
25	FOXP2	chr3:160938832-160939288	SK-N-MC	brain:	n/a	n/a
26	POLR2A	chr3:160938785-160939545	HepG2	liver:	n/a	n/a
27	POLR2A	chr3:160938604-160939422	PFSK-1	brain:	n/a	n/a
28	POLR2A	chr3:160938739-160939332	GM12891	blood:	n/a	n/a
29	POLR2A	chr3:160938727-160939893	HepG2	liver:	n/a	n/a
30	ELF1	chr3:160938677-160939711	MCF-7	breast:	n/a	chr3:160939264-160939276
31	MAX	chr3:160938417-160939855	A549	lung:	n/a	n/a
32	JUN	chr3:160938488-160939172	K562	blood:	n/a	chr3:160938885-160938899
33	POLR2A	chr3:160938710-160939508	GM12891	blood:	n/a	n/a
34	ZBTB33	chr3:160938732-160939387	A549	lung:	n/a	chr3:160938867-160938874 chr3:160939083-160939098
35	SIN3AK20	chr3:160938948-160939213	HepG2	liver:	n/a	n/a
36	POLR2A	chr3:160938583-160939595	K562	blood:	n/a	n/a
37	ELK4	chr3:160938863-160939187	Hela-S3	cervix:	n/a	n/a
38	POLR2A	chr3:160938617-160939716	PBDE	blood:	n/a	n/a
39	GTF2F1	chr3:160938560-160939306	Hela-S3	cervix:	n/a	n/a
40	POLR2A	chr3:160938803-160939385	GM12892	blood:	n/a	n/a
41	ZBTB33	chr3:160938833-160939311	K562	blood:	n/a	chr3:160938867-160938874 chr3:160939083-160939098
42	NR2F2	chr3:160938686-160939722	MCF-7	breast:	n/a	n/a
43	CREB1	chr3:160938876-160939267	ECC-1	luminal epithelium:	n/a	n/a
44	MAX	chr3:160938814-160939594	H1-hESC	embryonic stem cell:	n/a	n/a
45	TAF1	chr3:160938840-160939589	HepG2	liver:	n/a	n/a
46	POLR2A	chr3:160938760-160939613	GM18526	blood:	n/a	n/a
47	POLR2A	chr3:160938665-160939617	GM12891	blood:	n/a	n/a
48	RUNX3	chr3:160938752-160939617	GM12878	blood:	n/a	n/a
49	POLR2A	chr3:160938587-160939517	HUVEC	blood vessel:	n/a	n/a
50	MYC	chr3:160938669-160939615	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:160937993..160941056-chr3:161047965..161051023,3	MCF-7	breast:
2	chr3:160818503..160825890-chr3:160937051..160945986,18	MCF-7	breast:
3	chr19:12902198..12902786-chr3:160938697..160939572,2	Hela-S3	cervix:
4	chr11:74459661..74460383-chr3:160938597..160939219,2	Hela-S3	cervix:
5	chr3:160938091..160940577-chr7:104653089..104654973,2	MCF-7	breast:
6	chr3:160934982..160947568-chr3:161079696..161093037,40	MCF-7	breast:
7	chr12:123319135..123321319-chr3:160936978..160939441,2	MCF-7	breast:
8	chr3:160936365..160960187-chr3:161078472..161094658,51	MCF-7	breast:
9	chr3:160816932..160819441-chr3:160937058..160940131,3	MCF-7	breast:
10	chr3:160821182..160827138-chr3:160937374..160941314,7	MCF-7	breast:

Variant related genes	Relation type
NMD3	TF binding region
ENSG00000005483	Chromatin interaction
ENSG00000239569	Chromatin interaction
ENSG00000169255	Chromatin interaction
ENSG00000228393	Chromatin interaction
ENSG00000130787	Chromatin interaction
ENSG00000196542	Chromatin interaction
ENSG00000169251	Chromatin interaction
ENSG00000243838	Chromatin interaction
ENSG00000166439	Chromatin interaction
ENSG00000171223	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs1017799	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs12486069	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12486111	1.00[ASW][hapmap];1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.81[AMR][1000 genomes]
rs12486998	1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs12487002	0.89[JPT][hapmap]
rs12488127	1.00[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap]
rs12489004	1.00[CHB][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12489125	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12494520	0.84[AMR][1000 genomes]
rs12494725	0.83[ASN][1000 genomes]
rs12496235	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12496837	0.87[AMR][1000 genomes]
rs13315320	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs13319558	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13319771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1450518	0.88[JPT][hapmap]
rs16831850	1.00[GIH][hapmap];0.87[ASN][1000 genomes]
rs16831864	0.87[ASN][1000 genomes]
rs16831882	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs16831942	0.93[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2306209	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs28451189	0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs28704960	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs28713364	0.82[AMR][1000 genomes]
rs3925722	0.81[ASN][1000 genomes]
rs4296611	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4352387	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4468992	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4580574	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4635725	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs57903480	0.97[ASN][1000 genomes]
rs59567999	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs59757775	0.93[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs59776766	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59867530	0.90[AMR][1000 genomes]
rs60121330	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs6441350	1.00[GIH][hapmap];0.87[ASN][1000 genomes]
rs6441365	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6441372	1.00[ASN][1000 genomes]
rs6441375	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs6762064	1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6774919	0.85[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs6775446	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6775931	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6778186	1.00[ASN][1000 genomes]
rs6782415	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6782518	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6785714	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6787447	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6788738	0.82[AMR][1000 genomes]
rs6790805	1.00[ASN][1000 genomes]
rs6794601	0.89[JPT][hapmap]
rs6796168	0.87[ASN][1000 genomes]
rs6801664	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6805976	0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs73017340	1.00[ASN][1000 genomes]
rs73026933	0.97[ASN][1000 genomes]
rs73026967	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026968	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026983	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026987	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73026989	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs73878309	0.93[ASN][1000 genomes]
rs7615833	1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7615868	0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7624791	1.00[ASN][1000 genomes]
rs7626773	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7634299	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7651924	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs7652624	0.82[CHB][hapmap];1.00[ASN][1000 genomes]
rs9290070	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9290071	0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9810351	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9812574	0.93[ASN][1000 genomes]
rs9818470	1.00[ASN][1000 genomes]
rs9818835	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9818992	0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs9819793	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9822705	1.00[CHB][hapmap];0.88[JPT][hapmap];0.93[ASN][1000 genomes]
rs9822916	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9823424	0.87[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9824535	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9824805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9826857	1.00[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9830183	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9833270	1.00[GIH][hapmap];0.88[JPT][hapmap];0.91[MEX][hapmap];0.93[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9835530	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9838945	1.00[ASN][1000 genomes]
rs9841871	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9842290	1.00[ASN][1000 genomes]
rs9847842	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9850455	0.89[JPT][hapmap]
rs9851699	0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855112	0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9855572	0.93[ASN][1000 genomes]
rs9856742	0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9858907	0.81[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9859641	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9860980	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9862867	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs9871753	1.00[GIH][hapmap];0.88[JPT][hapmap];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9872514	0.89[JPT][hapmap]
rs9876077	1.00[ASN][1000 genomes]
rs9877309	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs9880536	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9884100	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9985364	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv931072	chr3:160669567-161159779	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1015063	chr3:160918307-161024070	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12490149	ENSG00000169251	cis	multi-tissue	Pritchard

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:160938000-160940400	Active TSS	Duodenum Smooth Muscle	Duodenum
2	chr3:160938200-160940400	Active TSS	A549	lung
3	chr3:160938200-160940600	Active TSS	Brain Cingulate Gyrus	brain
4	chr3:160938200-160940600	Active TSS	Brain Hippocampus Middle	brain
5	chr3:160938200-160940600	Active TSS	Right Atrium	heart
6	chr3:160938200-160940600	Active TSS	Thymus	Thymus
7	chr3:160938200-160940600	Active TSS	HSMM	muscle
8	chr3:160938400-160939200	Active TSS	Fetal Brain Female	brain
9	chr3:160938400-160939600	Active TSS	Primary B cells from cord blood	blood
10	chr3:160938400-160939800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
11	chr3:160938400-160940000	Active TSS	Monocytes-CD14+_RO01746	blood
12	chr3:160938400-160940400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:160938400-160940400	Active TSS	HUES6 Cell Line	embryonic stem cell
14	chr3:160938400-160940400	Active TSS	Rectal Mucosa Donor 29	rectum
15	chr3:160938400-160940600	Active TSS	ES-I3 Cell Line	embryonic stem cell
16	chr3:160938400-160940600	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:160938400-160940600	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:160938400-160940600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr3:160938400-160940600	Active TSS	GM12878-XiMat	blood
20	chr3:160938400-160940600	Active TSS	NH-A	brain
21	chr3:160938400-160940800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr3:160938400-160941200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr3:160938400-160941400	Active TSS	iPS-18 Cell Line	embryonic stem cell
24	chr3:160938400-160941600	Active TSS	Stomach Smooth Muscle	stomach
25	chr3:160938600-160939200	Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr3:160938600-160939200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr3:160938600-160939400	Active TSS	HepG2	liver
28	chr3:160938600-160939800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
29	chr3:160938600-160939800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr3:160938600-160940000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr3:160938600-160940000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:160938600-160940000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr3:160938600-160940000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
34	chr3:160938600-160940200	Active TSS	Placenta	Placenta
35	chr3:160938600-160940400	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:160938600-160940400	Active TSS	HUES48 Cell Line	embryonic stem cell
37	chr3:160938600-160940400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:160938600-160940400	Active TSS	Brain Angular Gyrus	brain
39	chr3:160938600-160940600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr3:160938600-160940600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr3:160938600-160940600	Active TSS	Brain Anterior Caudate	brain
42	chr3:160938600-160940600	Active TSS	Fetal Intestine Large	intestine
43	chr3:160938600-160940600	Active TSS	Fetal Thymus	thymus
44	chr3:160938600-160940600	Active TSS	Left Ventricle	heart
45	chr3:160938600-160940600	Active TSS	Ovary	ovary
46	chr3:160938600-160940600	Active TSS	Psoas Muscle	Psoas
47	chr3:160938600-160940600	Active TSS	Skeletal Muscle Female	skeletal muscle
48	chr3:160938600-160940800	Active TSS	H9 Cell Line	embryonic stem cell
49	chr3:160938600-160940800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr3:160938600-160940800	Active TSS	Breast Myoepithelial Primary Cells	Breast

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