Variant report

Variant	rs10279308
Chromosome Location	chr7:99005506-99005507
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:139)
CpG islands
(count:0)
Chromatin interactive
region (count:29)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:139 , 50 per page) page: 1 2 3

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99004959-99007064	PFSK-1	brain:	n/a	n/a
2	MXI1	chr7:99005332-99007193	HepG2	liver:	n/a	chr7:99006650-99006665 chr7:99006652-99006667
3	MAX	chr7:99005308-99006963	HepG2	liver:	n/a	n/a
4	MAX	chr7:99005267-99006859	ECC-1	luminal epithelium:	n/a	n/a
5	PML	chr7:99005413-99007342	GM12878	blood:	n/a	chr7:99005829-99005838
6	BRCA1	chr7:99005458-99006661	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr7:99005447-99005891	HepG2	liver:	n/a	n/a
8	SMARCC1	chr7:99005369-99007295	Hela-S3	cervix:	n/a	chr7:99005830-99005839
9	POLR2A	chr7:99005506-99007025	K562	blood:	n/a	n/a
10	POLR2A	chr7:99003969-99007015	SK-N-MC	brain:	n/a	n/a
11	SIN3AK20	chr7:99005503-99005758	HepG2	liver:	n/a	n/a
12	SIN3AK20	chr7:99005123-99007151	MCF-7	breast:	n/a	n/a
13	POLR2A	chr7:99005187-99007322	GM12892	blood:	n/a	n/a
14	MTA3	chr7:99004942-99007455	GM12878	blood:	n/a	n/a
15	MYC	chr7:99005344-99006719	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr7:99004884-99006880	PFSK-1	brain:	n/a	n/a
17	MYC	chr7:99005420-99006994	Hela-S3	cervix:	n/a	n/a
18	MAX	chr7:99005378-99006905	Hela-S3	cervix:	n/a	n/a
19	GTF2F1	chr7:99005359-99005950	Hela-S3	cervix:	n/a	n/a
20	POLR2A	chr7:99004847-99007309	K562	blood:	n/a	n/a
21	POLR2A	chr7:99005398-99006928	GM12878	blood:	n/a	n/a
22	TBP	chr7:99005500-99006977	K562	blood:	n/a	n/a
23	POLR2A	chr7:99004851-99007425	H1-hESC	embryonic stem cell:	n/a	n/a
24	MAX	chr7:99005358-99005778	H1-hESC	embryonic stem cell:	n/a	n/a
25	JUND	chr7:99003803-99007899	SK-N-SH	brain:	n/a	chr7:99007393-99007402 chr7:99005830-99005840 chr7:99007390-99007399 chr7:99005830-99005840 chr7:99005831-99005839 chr7:99005830-99005840 chr7:99005830-99005840 chr7:99007391-99007400
26	E2F6	chr7:99005436-99006802	K562	blood:	n/a	chr7:99006261-99006271 chr7:99006267-99006277 chr7:99006264-99006274 chr7:99006346-99006355
27	POLR2A	chr7:99005362-99006991	GM12891	blood:	n/a	n/a
28	POLR2A	chr7:99005442-99007036	H1-hESC	embryonic stem cell:	n/a	n/a
29	POLR2A	chr7:99005250-99006031	A549	lung:	n/a	n/a
30	MYC	chr7:99005506-99005773	HepG2	liver:	n/a	n/a
31	POLR2A	chr7:99005219-99007100	GM12892	blood:	n/a	n/a
32	POLR2A	chr7:99003742-99007162	SK-N-SH	brain:	n/a	n/a
33	MAX	chr7:99005327-99006891	A549	lung:	n/a	n/a
34	MXI1	chr7:99005077-99007229	GM12878	blood:	n/a	chr7:99006650-99006665 chr7:99006652-99006667
35	NR2F2	chr7:99004834-99007401	K562	blood:	n/a	n/a
36	POLR2A	chr7:99005030-99006994	U87	brain:	n/a	n/a
37	POLR2A	chr7:99004714-99006984	PANC-1	pancreas:	n/a	n/a
38	POLR2A	chr7:99004668-99007732	IMR90	lung:	n/a	n/a
39	GABPA	chr7:99005169-99007388	MCF-7	breast:	n/a	chr7:99006142-99006151
40	MXI1	chr7:99005401-99005948	K562	blood:	n/a	n/a
41	MAX	chr7:99005283-99007032	SK-N-SH	brain:	n/a	n/a
42	MAX	chr7:99005391-99005905	A549	lung:	n/a	n/a
43	MYC	chr7:99005432-99007202	K562	blood:	n/a	n/a
44	MYC	chr7:99005386-99007109	K562	blood:	n/a	n/a
45	HEY1	chr7:99005119-99007211	K562	blood:	n/a	chr7:99006526-99006541
46	MAX	chr7:99005168-99007014	A549	lung:	n/a	n/a
47	POLR2A	chr7:99005455-99007190	PBDE	blood:	n/a	n/a
48	HEY1	chr7:99005470-99006918	HepG2	liver:	n/a	chr7:99006526-99006541
49	POLR2A	chr7:99005493-99006952	Hela-S3	cervix:	n/a	n/a
50	EP300	chr7:99005401-99006993	SK-N-SH	brain:	n/a	chr7:99006142-99006151 chr7:99006442-99006449 chr7:99006264-99006273 chr7:99006267-99006276

No data

(count:29 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99004073..99007178-chr7:99034881..99037749,7	MCF-7	breast:
2	chr7:99005493..99007248-chr7:99698114..99700010,2	MCF-7	breast:
3	chr7:99004812..99006640-chr7:99069621..99072318,3	K562	blood:
4	chr7:99004301..99006264-chr7:99095120..99098080,2	MCF-7	breast:
5	chr7:99004207..99009187-chr7:99032699..99039268,13	MCF-7	breast:
6	chr7:98981776..98988825-chr7:99001775..99008244,9	K562	blood:
7	chr17:57917415..57919234-chr7:99005336..99006972,2	MCF-7	breast:
8	chr7:98963718..98966584-chr7:99003795..99005637,2	MCF-7	breast:
9	chr7:99004357..99007369-chr7:99061400..99065046,4	K562	blood:
10	chr7:99004290..99006114-chr7:99025633..99027496,2	K562	blood:
11	chr17:59938658..59940749-chr7:99004886..99006495,2	MCF-7	breast:
12	chr7:98921987..98924595-chr7:99004669..99006776,2	K562	blood:
13	chr13:111365372..111366015-chr7:99005101..99005601,2	Hela-S3	cervix:
14	chr7:99004357..99008691-chr7:99061400..99066308,7	K562	blood:
15	chr7:99005276..99007163-chr7:99100557..99104017,3	K562	blood:
16	chr7:98988826..98993566-chr7:99002963..99006762,7	MCF-7	breast:
17	chr21:41754491..41756003-chr7:99004951..99007138,2	MCF-7	breast:
18	chr7:99003930..99008101-chr7:99034839..99037079,5	K562	blood:
19	chr7:99005495..99008019-chr7:99062000..99063927,3	MCF-7	breast:
20	chr7:99004079..99005950-chr7:99029849..99032633,2	MCF-7	breast:
21	chr7:98968876..98974378-chr7:99004810..99008269,11	K562	blood:
22	chr7:98970407..98975516-chr7:99002028..99009396,17	MCF-7	breast:
23	chr7:99004598..99006577-chr7:99061839..99063802,3	MCF-7	breast:
24	chr7:98861668..98864470-chr7:99003441..99006106,2	K562	blood:
25	chr7:98986172..98988816-chr7:99004808..99007138,3	MCF-7	breast:
26	chr7:99005061..99007834-chr7:99068897..99070903,2	MCF-7	breast:
27	chr7:99004495..99006339-chr7:99697031..99698874,2	K562	blood:
28	chr17:57917564..57920084-chr7:99004805..99007004,2	MCF-7	breast:
29	chr7:98970740..98974571-chr7:99004724..99008680,16	MCF-7	breast:

No data

Variant related genes	Relation type
BUD31	TF binding region
PDAP1	TF binding region
ENSG00000160908	Chromatin interaction
ENSG00000002079	Chromatin interaction
ENSG00000198556	Chromatin interaction
ENSG00000235123	Chromatin interaction
ENSG00000221838	Chromatin interaction
ENSG00000166508	Chromatin interaction
ENSG00000136492	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000196652	Chromatin interaction
ENSG00000130429	Chromatin interaction
ENSG00000248919	Chromatin interaction
ENSG00000241468	Chromatin interaction
ENSG00000160917	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000106246	Chromatin interaction
ENSG00000241685	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs10155966	0.91[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs10225529	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10238965	0.84[CEU][hapmap]
rs10243678	0.91[CEU][hapmap];0.82[TSI][hapmap];0.87[EUR][1000 genomes]
rs10249167	0.82[EUR][1000 genomes]
rs10251282	0.95[ASN][1000 genomes]
rs10254729	0.91[CEU][hapmap]
rs10255399	0.81[EUR][1000 genomes]
rs10258757	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10270459	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs10270917	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs10271049	0.84[CEU][hapmap]
rs10272998	0.91[CEU][hapmap]
rs10277149	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1043466	0.84[CEU][hapmap]
rs1045012	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs10953288	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs11734	0.84[ASN][1000 genomes]
rs11762273	0.91[CEU][hapmap];0.83[EUR][1000 genomes]
rs11771702	0.91[CEU][hapmap]
rs11972017	0.83[MEX][hapmap]
rs11976018	0.84[CEU][hapmap]
rs11978089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12112936	0.91[CEU][hapmap]
rs12113440	0.91[CEU][hapmap]
rs12531852	0.84[TSI][hapmap]
rs12538893	0.81[CEU][hapmap]
rs17161662	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs17161669	0.81[CEU][hapmap];0.82[GIH][hapmap]
rs17161695	0.91[CEU][hapmap];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17161700	1.00[JPT][hapmap]
rs17161726	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs17854665	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs1980307	0.84[CEU][hapmap]
rs2003499	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2072181	0.91[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs2240384	0.84[CEU][hapmap]
rs2240385	0.94[YRI][hapmap]
rs2272168	0.84[CEU][hapmap]
rs2280600	0.84[CEU][hapmap]
rs2280601	0.84[CEU][hapmap]
rs2286162	0.91[CEU][hapmap]
rs2293256	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2404323	0.82[EUR][1000 genomes]
rs2404487	0.95[ASN][1000 genomes]
rs2404488	0.95[ASN][1000 genomes]
rs28377312	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28460612	0.95[ASN][1000 genomes]
rs28495024	0.85[EUR][1000 genomes]
rs28558950	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28668326	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs28753399	0.95[ASN][1000 genomes]
rs3137	0.84[CEU][hapmap]
rs34943973	0.95[ASN][1000 genomes]
rs3528	0.95[ASN][1000 genomes]
rs3800960	0.94[YRI][hapmap]
rs3801288	0.91[CEU][hapmap]
rs3823813	0.89[ASN][1000 genomes]
rs41385645	1.00[JPT][hapmap]
rs45441991	0.89[ASN][1000 genomes]
rs45448997	0.95[ASN][1000 genomes]
rs45451992	0.95[ASN][1000 genomes]
rs45461000	0.95[ASN][1000 genomes]
rs45492501	0.89[ASN][1000 genomes]
rs45529541	0.89[ASN][1000 genomes]
rs45555335	0.89[ASN][1000 genomes]
rs45592335	0.89[ASN][1000 genomes]
rs4729532	1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs55927283	0.89[ASN][1000 genomes]
rs55942267	0.95[ASN][1000 genomes]
rs56167514	0.89[ASN][1000 genomes]
rs57367781	0.89[ASN][1000 genomes]
rs59240302	0.89[ASN][1000 genomes]
rs59574285	0.84[ASN][1000 genomes]
rs59672032	0.95[ASN][1000 genomes]
rs6943920	0.91[CEU][hapmap];0.82[TSI][hapmap];0.84[EUR][1000 genomes]
rs6955490	1.00[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6957987	0.82[CEU][hapmap];0.83[MEX][hapmap]
rs6960810	0.84[TSI][hapmap]
rs6962772	0.84[CEU][hapmap]
rs6974831	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs73397447	0.95[ASN][1000 genomes]
rs73397481	0.95[ASN][1000 genomes]
rs73397499	0.95[ASN][1000 genomes]
rs733991	0.91[CEU][hapmap];0.82[GIH][hapmap];0.83[MEX][hapmap]
rs73401507	0.95[ASN][1000 genomes]
rs73401510	0.95[ASN][1000 genomes]
rs73401516	0.95[ASN][1000 genomes]
rs73403247	0.89[ASN][1000 genomes]
rs73403272	0.89[ASN][1000 genomes]
rs73403286	0.89[ASN][1000 genomes]
rs73403290	0.89[ASN][1000 genomes]
rs73405247	0.89[ASN][1000 genomes]
rs73711280	0.95[ASN][1000 genomes]
rs73711293	0.89[ASN][1000 genomes]
rs73711294	0.89[ASN][1000 genomes]
rs73713507	0.89[ASN][1000 genomes]
rs73713531	0.84[ASN][1000 genomes]
rs7794068	0.89[ASN][1000 genomes]
rs7794705	0.84[CEU][hapmap]
rs7805661	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs883403	0.84[CEU][hapmap]
rs917152	1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs917154	0.83[CEU][hapmap]
rs940336	0.83[YRI][hapmap]
rs952319	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs9969217	0.82[GIH][hapmap];0.83[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3433144	chr7:98777878-99060209	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv831068	chr7:98819572-99006481	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv831069	chr7:98948128-99127584	Active TSS Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs10279308	ZKSCAN1	cis	parietal	SCAN
rs10279308	OR2AE1	cis	parietal	SCAN
rs10279308	PILRB	cis	lymphoblastoid	GTEx
rs10279308	CPSF4	cis	parietal	SCAN
rs10279308	GATS	cis	parietal	SCAN
rs10279308	STAG3	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99004000-99005600	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr7:99004200-99005600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr7:99004200-99005600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr7:99004200-99005600	Flanking Active TSS	Dnd41	blood
5	chr7:99004200-99005600	Flanking Active TSS	HUVEC	blood vessel
6	chr7:99004200-99008000	Active TSS	HUES6 Cell Line	embryonic stem cell
7	chr7:99004400-99005600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
8	chr7:99004400-99005600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr7:99004400-99005600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
10	chr7:99004400-99005600	Flanking Active TSS	Osteobl	bone
11	chr7:99004400-99005800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr7:99004400-99005800	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr7:99004600-99005600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr7:99004600-99005600	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr7:99004600-99005600	Flanking Active TSS	Colon Smooth Muscle	Colon
16	chr7:99004600-99005600	Flanking Active TSS	Fetal Brain Female	brain
17	chr7:99004600-99005800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr7:99004600-99005800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr7:99004600-99005800	Flanking Active TSS	Stomach Smooth Muscle	stomach
20	chr7:99004600-99007600	Active TSS	H1 Cell Line	embryonic stem cell
21	chr7:99004600-99007800	Active TSS	Psoas Muscle	Psoas
22	chr7:99004600-99008000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr7:99004800-99005600	Flanking Active TSS	Brain Cingulate Gyrus	brain
24	chr7:99004800-99005600	Flanking Active TSS	Brain Hippocampus Middle	brain
25	chr7:99004800-99005600	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr7:99004800-99005600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr7:99004800-99005600	Flanking Active TSS	NH-A	brain
28	chr7:99004800-99005800	Flanking Active TSS	Liver	Liver
29	chr7:99004800-99005800	Flanking Active TSS	Fetal Thymus	thymus
30	chr7:99004800-99006000	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
31	chr7:99004800-99006000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
32	chr7:99004800-99006200	Flanking Active TSS	Primary hematopoietic stem cells	blood
33	chr7:99004800-99006200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr7:99004800-99007600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
35	chr7:99004800-99007600	Active TSS	Aorta	Aorta
36	chr7:99005000-99005600	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr7:99005000-99005600	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
38	chr7:99005000-99005600	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
39	chr7:99005000-99005600	Flanking Active TSS	Brain Angular Gyrus	brain
40	chr7:99005000-99005600	Flanking Active TSS	Brain Anterior Caudate	brain
41	chr7:99005000-99005600	Flanking Active TSS	Brain Germinal Matrix	brain
42	chr7:99005000-99005600	Flanking Active TSS	Colonic Mucosa	Colon
43	chr7:99005000-99005600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
44	chr7:99005000-99005600	Flanking Active TSS	Fetal Muscle Leg	muscle
45	chr7:99005000-99005600	Flanking Active TSS	Fetal Stomach	stomach
46	chr7:99005000-99005800	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
47	chr7:99005000-99005800	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
48	chr7:99005000-99005800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
49	chr7:99005000-99005800	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
50	chr7:99005000-99005800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

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