Variant report

Variant	rs9881491
Chromosome Location	chr3:48487911-48487912
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:332)
CpG islands
(count:0)
Chromatin interactive
region (count:24)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:332 , 50 per page) page: 1 2 3 4 5 6 7

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	SRF	chr3:48487806-48488346	H1-hESC	embryonic stem cell:	n/a	n/a
2	CREB1	chr3:48487480-48488656	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48487654-48488717	PBDE	blood:	n/a	n/a
4	HA-E2F1	chr3:48487632-48488884	MCF-7	breast:	n/a	chr3:48488160-48488169 chr3:48488113-48488122 chr3:48488063-48488072
5	POLR2A	chr3:48487805-48488585	A549	lung:	n/a	n/a
6	TAF1	chr3:48487801-48488414	K562	blood:	n/a	n/a
7	HEY1	chr3:48487740-48488564	K562	blood:	n/a	chr3:48488064-48488079 chr3:48488125-48488140 chr3:48488134-48488149
8	POLR2A	chr3:48487693-48488600	GM12878	blood:	n/a	n/a
9	FOXA1	chr3:48487843-48488522	HepG2	liver:	n/a	n/a
10	ARID3A	chr3:48487894-48488292	K562	blood:	n/a	n/a
11	UBTF	chr3:48487880-48488664	K562	blood:	n/a	n/a
12	MAX	chr3:48487649-48488687	SK-N-SH	brain:	n/a	n/a
13	TBP	chr3:48487712-48488628	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr3:48487748-48488675	GM18505	blood:	n/a	n/a
15	CHD2	chr3:48487877-48488617	H1-hESC	embryonic stem cell:	n/a	n/a
16	POU2F2	chr3:48487727-48488378	GM12891	blood:	n/a	n/a
17	KAP1	chr3:48487434-48488534	HEK293	kidney:	n/a	n/a
18	CEBPD	chr3:48487863-48488380	HepG2	liver:	n/a	n/a
19	POLR2A	chr3:48487746-48488646	HepG2	liver:	n/a	n/a
20	POLR2A	chr3:48487658-48488733	H1-neurons	neurons:	n/a	n/a
21	ATF3	chr3:48487873-48488291	H1-hESC	embryonic stem cell:	n/a	chr3:48488162-48488171
22	SP1	chr3:48487895-48488294	GM12878	blood:	n/a	chr3:48488130-48488140 chr3:48488131-48488140 chr3:48488129-48488140 chr3:48488130-48488139 chr3:48488129-48488141 chr3:48488131-48488140 chr3:48488129-48488141 chr3:48488130-48488140
23	POLR2A	chr3:48487669-48488742	Hela-S3	cervix:	n/a	n/a
24	YY1	chr3:48487787-48488635	K562	blood:	n/a	n/a
25	POLR2A	chr3:48487800-48488664	K562	blood:	n/a	n/a
26	POLR2A	chr3:48487773-48488556	GM18526	blood:	n/a	n/a
27	MYC	chr3:48487807-48488671	K562	blood:	n/a	n/a
28	POLR2A	chr3:48487782-48488699	HepG2	liver:	n/a	n/a
29	REST	chr3:48487855-48488301	HepG2	liver:	n/a	chr3:48488122-48488135
30	TCF12	chr3:48487827-48488373	GM12878	blood:	n/a	chr3:48488107-48488114
31	SIN3AK20	chr3:48487559-48488926	HCT-116	colon:	n/a	n/a
32	POLR2A	chr3:48487754-48488582	GM18951	blood:	n/a	n/a
33	YY1	chr3:48487865-48488388	SK-N-SH_RA	brain:	n/a	n/a
34	TAF1	chr3:48487686-48488725	ECC-1	luminal epithelium:	n/a	n/a
35	TCF12	chr3:48487897-48488214	H1-hESC	embryonic stem cell:	n/a	chr3:48488107-48488114
36	TAF1	chr3:48487720-48488435	GM12892	blood:	n/a	n/a
37	CREB1	chr3:48487799-48488300	ECC-1	luminal epithelium:	n/a	n/a
38	SIN3A	chr3:48487866-48488626	GM12878	blood:	n/a	n/a
39	POLR2A	chr3:48485860-48488666	GM12891	blood:	n/a	n/a
40	TAF1	chr3:48487714-48488617	HepG2	liver:	n/a	n/a
41	CREB1	chr3:48487638-48488652	HepG2	liver:	n/a	n/a
42	POLR2A	chr3:48487790-48488637	GM12892	blood:	n/a	n/a
43	POLR2A	chr3:48487707-48488590	GM12878	blood:	n/a	n/a
44	POLR2A	chr3:48487806-48488865	K562	blood:	n/a	n/a
45	PML	chr3:48487801-48488438	K562	blood:	n/a	n/a
46	PML	chr3:48487911-48488343	GM12878	blood:	n/a	n/a
47	CREB1	chr3:48487578-48488777	HepG2	liver:	n/a	n/a
48	ELF1	chr3:48487754-48488629	GM12878	blood:	n/a	chr3:48488092-48488104
49	TAF7	chr3:48487791-48488589	H1-hESC	embryonic stem cell:	n/a	n/a
50	SMARCB1	chr3:48487753-48488611	Hela-S3	cervix:	n/a	n/a

No data

(count:24 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:48469445..48473059-chr3:48486174..48489531,5	MCF-7	breast:
2	chr3:48460976..48462671-chr3:48486369..48489165,2	MCF-7	breast:
3	chr3:48487745..48490928-chr3:48507452..48510660,3	K562	blood:
4	chr3:48412970..48414853-chr3:48487087..48489637,2	K562	blood:
5	chr3:48477555..48484761-chr3:48484855..48490000,13	MCF-7	breast:
6	chr3:48487725..48489433-chr3:48594364..48597196,2	MCF-7	breast:
7	chr1:173836756..173837524-chr3:48487822..48488444,2	Hela-S3	cervix:
8	chr3:48468360..48471756-chr3:48485148..48489754,5	K562	blood:
9	chr3:48486835..48489928-chr3:48540255..48543800,6	MCF-7	breast:
10	chr3:48469539..48472280-chr3:48487900..48489460,2	MCF-7	breast:
11	chr3:48486334..48488063-chr3:48594171..48595954,2	MCF-7	breast:
12	chr3:48486933..48489526-chr3:48585390..48587565,2	MCF-7	breast:
13	chr3:48485967..48488247-chr3:48600373..48602900,2	MCF-7	breast:
14	chr3:48486214..48489756-chr3:48493754..48497547,4	K562	blood:
15	chr3:48484123..48488497-chr3:48591865..48597132,6	K562	blood:
16	chr3:48485548..48495296-chr3:48503776..48510303,13	MCF-7	breast:
17	chr3:48227952..48230127-chr3:48487566..48489526,2	K562	blood:
18	chr3:48341768..48344382-chr3:48487005..48489358,2	K562	blood:
19	chr3:48227952..48231564-chr3:48487479..48489526,3	K562	blood:
20	chr3:48486535..48489941-chr3:48491977..48496128,7	MCF-7	breast:
21	chr3:48341910..48343501-chr3:48486949..48488485,2	MCF-7	breast:
22	chr3:48487800..48488607-chr5:179233338..179233841,2	Hela-S3	cervix:
23	chr11:62609196..62609700-chr3:48487799..48488439,2	NB4	blood:
24	chr3:48487008..48490928-chr3:48507402..48510491,5	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CCDC51-1	chr3:48487738-48488060	ENSG00000244380.1
2	lnc-CCDC51-1	chr3:48487663-48488036	ENSG00000244380.1

No data

Variant related genes	Relation type
ATRIP	TF binding region
ENSG00000185278	Chromatin interaction
ENSG00000164054	Chromatin interaction
ENSG00000164045	Chromatin interaction
ENSG00000114268	Chromatin interaction
ENSG00000164050	Chromatin interaction
ENSG00000164051	Chromatin interaction
ENSG00000172113	Chromatin interaction
ENSG00000145040	Chromatin interaction
ENSG00000164053	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000161011	Chromatin interaction
ENSG00000114270	Chromatin interaction
ENSG00000232112	Chromatin interaction
ENSG00000133316	Chromatin interaction
ENSG00000234741	Chromatin interaction
ENSG00000164049	Chromatin interaction
ENSG00000161013	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1037773	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10470686	0.95[EUR][1000 genomes]
rs1109227	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11130170	0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs11130171	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11712561	0.90[AFR][1000 genomes];0.93[EUR][1000 genomes]
rs11797	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12487542	0.93[EUR][1000 genomes]
rs13069724	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13071337	0.94[EUR][1000 genomes]
rs13072012	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13076076	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13091785	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13314659	0.95[EUR][1000 genomes]
rs13324374	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459242	0.88[EUR][1000 genomes]
rs1459249	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1459250	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1563736	0.94[EUR][1000 genomes]
rs1824363	0.80[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1870444	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1975844	0.94[EUR][1000 genomes]
rs2045554	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2242150	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279077	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2290822	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2362450	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2362452	0.88[EUR][1000 genomes]
rs28824259	0.94[EUR][1000 genomes]
rs2885509	0.89[EUR][1000 genomes]
rs2885510	0.89[EUR][1000 genomes]
rs3214041	0.95[EUR][1000 genomes]
rs34761139	0.94[EUR][1000 genomes]
rs35215722	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3774808	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4490383	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4858793	0.89[EUR][1000 genomes]
rs4858817	0.89[EUR][1000 genomes]
rs60512868	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442116	0.88[EUR][1000 genomes]
rs6442117	0.91[EUR][1000 genomes]
rs6442118	0.95[EUR][1000 genomes]
rs6442119	0.95[EUR][1000 genomes]
rs6442120	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6442123	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6442124	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6764415	0.85[EUR][1000 genomes]
rs6770470	0.93[EUR][1000 genomes]
rs6776700	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779262	0.89[EUR][1000 genomes]
rs6784322	0.92[EUR][1000 genomes]
rs6784541	0.92[EUR][1000 genomes]
rs6794875	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6796491	0.94[EUR][1000 genomes]
rs6800475	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6804774	0.94[EUR][1000 genomes]
rs6810060	0.93[EUR][1000 genomes]
rs7126	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs725309	0.89[EUR][1000 genomes]
rs725310	0.89[EUR][1000 genomes]
rs73074358	0.93[EUR][1000 genomes]
rs734072	0.81[AMR][1000 genomes]
rs7618883	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7630741	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7634377	0.92[EUR][1000 genomes]
rs7635522	0.93[EUR][1000 genomes]
rs7636044	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7636782	0.91[EUR][1000 genomes]
rs7639743	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7653691	0.90[EUR][1000 genomes]
rs898225	0.88[EUR][1000 genomes]
rs922075	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9311423	0.92[EUR][1000 genomes]
rs9311424	0.92[EUR][1000 genomes]
rs9809843	0.94[EUR][1000 genomes]
rs9812647	0.95[EUR][1000 genomes]
rs9815088	0.80[AMR][1000 genomes]
rs9815103	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9817615	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9826195	0.94[EUR][1000 genomes]
rs9826247	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838618	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9849509	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9862575	0.94[EUR][1000 genomes]
rs9864371	0.89[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs9864815	0.94[EUR][1000 genomes]
rs9875280	0.94[EUR][1000 genomes]
rs9876781	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9876891	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9883759	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9883927	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834683	chr3:48301504-48493261	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
4	nsv876761	chr3:48464968-48496758	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9881491	TMA7	cis	Muscle Skeletal	GTEx
rs9881491	RP11-24C3.2	cis	Muscle Skeletal	GTEx
rs9881491	TREX1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48486400-48488200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr3:48486800-48488600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr3:48486800-48488800	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr3:48486800-48489000	Active TSS	iPS-20b Cell Line	embryonic stem cell
5	chr3:48486800-48489600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr3:48487000-48488000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr3:48487200-48488000	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:48487200-48488000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
9	chr3:48487200-48488000	Flanking Active TSS	Primary T cells from cord blood	blood
10	chr3:48487200-48488000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr3:48487200-48488000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
12	chr3:48487200-48488000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr3:48487200-48488000	Flanking Active TSS	Stomach Smooth Muscle	stomach
14	chr3:48487200-48488000	Flanking Active TSS	GM12878-XiMat	blood
15	chr3:48487200-48488000	Flanking Active TSS	HMEC	breast
16	chr3:48487200-48488000	Flanking Active TSS	HUVEC	blood vessel
17	chr3:48487200-48488000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
18	chr3:48487200-48488000	Flanking Active TSS	NH-A	brain
19	chr3:48487200-48488800	Active TSS	iPS-18 Cell Line	embryonic stem cell
20	chr3:48487200-48489000	Active TSS	ES-I3 Cell Line	embryonic stem cell
21	chr3:48487200-48489200	Active TSS	H9 Cell Line	embryonic stem cell
22	chr3:48487400-48488000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
23	chr3:48487400-48488000	Flanking Active TSS	Primary B cells from cord blood	blood
24	chr3:48487400-48488000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
25	chr3:48487400-48488000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
26	chr3:48487400-48488000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
27	chr3:48487400-48488000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr3:48487400-48488000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
29	chr3:48487400-48488000	Flanking Active TSS	Adipose Nuclei	Adipose
30	chr3:48487400-48488000	Flanking Active TSS	Liver	Liver
31	chr3:48487400-48488000	Flanking Active TSS	Colonic Mucosa	Colon
32	chr3:48487400-48488000	Flanking Active TSS	Duodenum Mucosa	Duodenum
33	chr3:48487400-48488000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
34	chr3:48487400-48488000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr3:48487400-48488600	Active TSS	Brain Germinal Matrix	brain
36	chr3:48487400-48488800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
37	chr3:48487400-48488800	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:48487400-48488800	Active TSS	K562	blood
39	chr3:48487400-48488800	Active TSS	NHLF	lung
40	chr3:48487400-48489000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
41	chr3:48487400-48489000	Active TSS	iPS-15b Cell Line	embryonic stem cell
42	chr3:48487400-48489000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr3:48487400-48489000	Active TSS	Left Ventricle	heart
44	chr3:48487400-48489200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:48487600-48488000	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr3:48487600-48488000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
47	chr3:48487600-48488000	Flanking Active TSS	Primary B cells from peripheral blood	blood
48	chr3:48487600-48488000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
49	chr3:48487600-48488000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
50	chr3:48487600-48488000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood

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