Variant report

Variant	rs9900074
Chromosome Location	chr17:46124326-46124327
allele	C/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	POLR2A	chr17:46124277-46126855	GM12892	blood:	n/a	n/a
2	MAX	chr17:46124297-46126790	A549	lung:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
3	POLR2A	chr17:46124081-46124531	K562	blood:	n/a	n/a
4	STAT3	chr17:46124294-46124780	MCF10A-Er-Src	breast:	n/a	chr17:46124561-46124570
5	POLR2A	chr17:46124024-46126770	PFSK-1	brain:	n/a	n/a
6	SIN3AK20	chr17:46123914-46126967	MCF-7	breast:	n/a	n/a
7	POLR2A	chr17:46124215-46126844	U87	brain:	n/a	n/a
8	POLR2A	chr17:46124261-46126838	U87	brain:	n/a	n/a
9	MXI1	chr17:46121714-46126967	SK-N-SH	brain:	n/a	n/a
10	REST	chr17:46124284-46126689	A549	lung:	n/a	chr17:46125042-46125062 chr17:46125048-46125062
11	POLR2A	chr17:46124215-46124483	HUVEC	blood vessel:	n/a	n/a
12	POLR2A	chr17:46122734-46126909	MCF10A-Er-Src	breast:	n/a	n/a
13	CHD1	chr17:46124061-46127653	IMR90	lung:	n/a	chr17:46125708-46125718
14	HCFC1	chr17:46124196-46127588	Hela-S3	cervix:	n/a	n/a
15	MTA3	chr17:46124305-46126831	GM12878	blood:	n/a	n/a
16	POLR2A	chr17:46124087-46127425	GM12878	blood:	n/a	n/a
17	POLR2A	chr17:46123986-46128643	MCF10A-Er-Src	breast:	n/a	n/a
18	POLR2A	chr17:46124116-46126774	GM12891	blood:	n/a	n/a
19	POLR2A	chr17:46123942-46126672	PANC-1	pancreas:	n/a	n/a
20	POLR2A	chr17:46124214-46126823	HUVEC	blood vessel:	n/a	n/a
21	IRF1	chr17:46124302-46126353	K562	blood:	n/a	chr17:46125915-46125929 chr17:46125706-46125720
22	MAX	chr17:46124107-46126723	SK-N-SH	brain:	n/a	chr17:46125917-46125927 chr17:46125705-46125715 chr17:46125209-46125219 chr17:46125627-46125637
23	PBX3	chr17:46124309-46126459	SK-N-SH	brain:	n/a	chr17:46125599-46125608 chr17:46125586-46125606
24	ZMIZ1	chr17:46124251-46124576	K562	blood:	n/a	n/a
25	TEAD4	chr17:46124223-46126698	K562	blood:	n/a	chr17:46125837-46125846
26	POLR2A	chr17:46124062-46127279	GM12878	blood:	n/a	n/a
27	POLR2A	chr17:46123447-46126752	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr17:46124314-46126749	GM12891	blood:	n/a	n/a
29	POLR2A	chr17:46121736-46126744	K562	blood:	n/a	n/a
30	POLR2A	chr17:46124178-46124362	HepG2	liver:	n/a	n/a
31	POLR2A	chr17:46124297-46126774	GM12878	blood:	n/a	n/a
32	JUN	chr17:46122472-46126784	K562	blood:	n/a	chr17:46125601-46125610 chr17:46125499-46125508 chr17:46124562-46124569 chr17:46124562-46124571 chr17:46125676-46125685 chr17:46124353-46124365
33	POLR2A	chr17:46124282-46126472	K562	blood:	n/a	n/a
34	FOSL2	chr17:46124169-46126769	A549	lung:	n/a	chr17:46125601-46125610 chr17:46125499-46125508 chr17:46124562-46124569 chr17:46124562-46124571 chr17:46125676-46125685 chr17:46124353-46124365

No.	Distal block	Cell Line	Cell type
1	chr17:46048551..46050173-chr17:46123931..46126830,2	MCF-7	breast:
2	chr17:46123351..46126971-chr17:46177351..46182209,7	K562	blood:
3	chr17:46034205..46036701-chr17:46124057..46126410,2	MCF-7	breast:
4	chr17:46123851..46125972-chr17:46688272..46690385,2	MCF-7	breast:
5	chr17:46124025..46127922-chr17:46176725..46180326,7	MCF-7	breast:
6	chr17:46124058..46125825-chr2:122286803..122289670,2	K562	blood:
7	chr17:46052757..46054496-chr17:46123061..46125014,2	K562	blood:
8	chr17:46123925..46127532-chr17:46701622..46704234,4	K562	blood:
9	chr17:46123538..46128867-chr17:46183649..46187295,7	MCF-7	breast:
10	chr17:46122869..46127022-chr17:46176971..46180616,11	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-COPZ2-1	chr17:46124281-46124669	XLOC_012503
2	lnc-COPZ2-1	chr17:46124254-46124332	XLOC_012503
3	lnc-COPZ2-1	chr17:46124321-46124332	XLOC_012503
4	lnc-COPZ2-1	chr17:46122503-46125412	ENSG00000263412.1
5	lnc-COPZ2-1	chr17:46124026-46125423	NONHSAT054369
6	lnc-COPZ2-1	chr17:46124314-46124332	NONHSAT054372
7	lnc-COPZ2-1	chr17:46124243-46124332	ENSG00000263412.1

Variant related genes	Relation type
NFE2L1	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000265451	Chromatin interaction
ENSG00000264229	Chromatin interaction
ENSG00000108468	Chromatin interaction
ENSG00000002919	Chromatin interaction
ENSG00000074054	Chromatin interaction
ENSG00000170689	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000260027	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10491182	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10491183	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1051001	0.98[EUR][1000 genomes]
rs11079805	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11079810	0.85[YRI][hapmap]
rs11079813	0.83[YRI][hapmap]
rs11650043	1.00[CEU][hapmap]
rs11650615	0.83[YRI][hapmap]
rs11651275	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11654292	0.84[YRI][hapmap]
rs11654342	0.82[AFR][1000 genomes]
rs11656818	0.98[EUR][1000 genomes]
rs11658242	0.87[YRI][hapmap]
rs12452399	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs16969990	1.00[CEU][hapmap]
rs17617360	1.00[CEU][hapmap]
rs17618704	1.00[CEU][hapmap]
rs17679445	1.00[CEU][hapmap]
rs1975703	0.85[YRI][hapmap]
rs28405789	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35091825	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41429650	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6504067	0.85[YRI][hapmap]
rs6504115	0.85[YRI][hapmap]
rs7209072	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7210041	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs7210671	0.88[YRI][hapmap]
rs7221897	0.81[YRI][hapmap]
rs7222646	0.83[YRI][hapmap]
rs7224155	0.83[YRI][hapmap]
rs8065797	0.85[YRI][hapmap];0.82[AFR][1000 genomes]
rs8067470	0.83[YRI][hapmap]
rs8071697	0.81[YRI][hapmap]
rs9890096	0.90[EUR][1000 genomes]
rs9893110	0.85[YRI][hapmap]
rs9895554	1.00[CEU][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9903963	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9905800	0.83[YRI][hapmap]
rs9909922	0.82[AFR][1000 genomes]
rs9914123	0.98[EUR][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	nsv469808	chr17:46049868-46228673	Enhancers Weak transcription Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases
2	nsv482897	chr17:46049868-46228673	Enhancers Active TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	85 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9900074	RP5-890E16.2	cis	Nerve Tibial	GTEx
rs9900074	PNPO	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:46121800-46124400	Enhancers	Fetal Muscle Leg	muscle
2	chr17:46122400-46124400	Enhancers	Adipose Nuclei	Adipose
3	chr17:46122600-46124400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr17:46122600-46124800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr17:46122600-46124800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
6	chr17:46122600-46124800	Flanking Active TSS	HSMM	muscle
7	chr17:46122600-46125000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr17:46122800-46124400	Enhancers	Colonic Mucosa	Colon
9	chr17:46122800-46124400	Enhancers	Rectal Mucosa Donor 31	rectum
10	chr17:46122800-46124400	Enhancers	Right Atrium	heart
11	chr17:46122800-46124600	Enhancers	Pancreas	Pancrea
12	chr17:46122800-46124600	Enhancers	Placenta Amnion	Placenta Amnion
13	chr17:46122800-46124600	Enhancers	HepG2	liver
14	chr17:46122800-46124800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr17:46122800-46125000	Flanking Active TSS	NHEK	skin
16	chr17:46123000-46124400	Enhancers	Fetal Intestine Small	intestine
17	chr17:46123000-46124600	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr17:46123000-46124800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr17:46123200-46124400	Enhancers	Primary T cells fromperipheralblood	blood
20	chr17:46123200-46124400	Weak transcription	Placenta	Placenta
21	chr17:46123200-46124600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr17:46123200-46124600	Enhancers	Stomach Mucosa	stomach
23	chr17:46123400-46124400	Weak transcription	Right Ventricle	heart
24	chr17:46123400-46124600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr17:46123400-46124600	Weak transcription	Lung	lung
26	chr17:46123400-46124800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr17:46123400-46125400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr17:46123600-46127200	Active TSS	HUES6 Cell Line	embryonic stem cell
29	chr17:46123800-46124400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr17:46123800-46124400	Enhancers	Primary monocytes fromperipheralblood	blood
31	chr17:46123800-46124400	Enhancers	Primary hematopoietic stem cells	blood
32	chr17:46123800-46124400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr17:46123800-46124400	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr17:46123800-46124400	Enhancers	Left Ventricle	heart
35	chr17:46123800-46124600	Enhancers	Small Intestine	intestine
36	chr17:46123800-46124800	Flanking Active TSS	Hela-S3	cervix
37	chr17:46123800-46127000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr17:46123800-46127600	Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr17:46124000-46124400	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
40	chr17:46124000-46124400	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr17:46124000-46124400	Enhancers	Primary B cells from peripheral blood	blood
42	chr17:46124000-46124400	Enhancers	Primary T helper naive cells from peripheral blood	blood
43	chr17:46124000-46124400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
44	chr17:46124000-46124400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
45	chr17:46124000-46124400	Enhancers	Primary T helper cells fromperipheralblood	blood
46	chr17:46124000-46124400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
47	chr17:46124000-46124400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
48	chr17:46124000-46124400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr17:46124000-46124400	Flanking Active TSS	Psoas Muscle	Psoas
50	chr17:46124000-46124600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links