Variant report

Variant	rs2003499
Chromosome Location	chr7:99014984-99014985
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:99014266-99018235	K562	blood:	n/a	n/a
2	POLR2A	chr7:99014945-99018503	GM12892	blood:	n/a	n/a
3	POLR2A	chr7:99014932-99018261	PFSK-1	brain:	n/a	n/a
4	POLR2A	chr7:99014890-99015651	K562	blood:	n/a	n/a
5	POLR2A	chr7:99013704-99019437	HepG2	liver:	n/a	n/a
6	POLR2A	chr7:99014422-99015683	GM12878	blood:	n/a	n/a
7	POLR2A	chr7:99014946-99015660	GM12891	blood:	n/a	n/a
8	POLR2A	chr7:99014979-99015605	U87	brain:	n/a	n/a
9	POLR2A	chr7:99014975-99015693	SK-N-SH	brain:	n/a	n/a
10	POLR2A	chr7:99014839-99015676	H1-hESC	embryonic stem cell:	n/a	n/a
11	POLR2A	chr7:99014958-99018400	PANC-1	pancreas:	n/a	n/a
12	POLR2A	chr7:99014953-99015616	Hela-S3	cervix:	n/a	n/a
13	POLR2A	chr7:99014910-99015724	GM12892	blood:	n/a	n/a
14	POLR2A	chr7:99014953-99019055	GM12878	blood:	n/a	n/a
15	POLR2A	chr7:99014547-99019035	SK-N-MC	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr7:99014925..99017023-chr7:99029378..99031176,2	K562	blood:
2	chr7:99014407..99016629-chr7:99032429..99035885,4	MCF-7	breast:
3	chr7:99014760..99017430-chr7:99030939..99032749,2	MCF-7	breast:
4	chr7:99014517..99016789-chr7:99055086..99057589,2	K562	blood:
5	chr7:99014835..99016757-chr7:99036121..99038779,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000239133	TF binding region
ENSG00000106246	Chromatin interaction
ENSG00000160917	Chromatin interaction

Extended variants
information (count: 113 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:111)

rs_ID	r²[population]
rs10155966	0.91[CEU][hapmap];0.82[TSI][hapmap];0.83[EUR][1000 genomes]
rs10225529	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10238965	0.84[CEU][hapmap]
rs10243678	0.91[CEU][hapmap];0.82[TSI][hapmap];0.85[EUR][1000 genomes]
rs10249167	0.81[EUR][1000 genomes]
rs10251282	0.95[ASN][1000 genomes]
rs10254729	0.91[CEU][hapmap]
rs10255399	0.80[EUR][1000 genomes]
rs10258757	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs10270459	0.91[CEU][hapmap];0.82[EUR][1000 genomes]
rs10270917	0.91[CEU][hapmap];0.80[EUR][1000 genomes]
rs10271049	0.84[CEU][hapmap]
rs10272998	0.91[CEU][hapmap]
rs10277149	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10279308	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]
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];0.82[EUR][1000 genomes]
rs11771702	0.91[CEU][hapmap]
rs11972017	0.83[MEX][hapmap]
rs11972210	1.00[JPT][hapmap]
rs11976018	0.84[CEU][hapmap]
rs11978089	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12112936	0.91[CEU][hapmap]
rs12113440	0.91[CEU][hapmap]
rs12531852	0.83[GIH][hapmap];0.84[TSI][hapmap]
rs12538893	0.81[CEU][hapmap]
rs17161662	0.81[CEU][hapmap]
rs17161669	0.81[CEU][hapmap]
rs17161695	0.91[CEU][hapmap];0.92[AMR][1000 genomes];0.87[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]
rs2072181	0.91[CEU][hapmap];0.82[TSI][hapmap];0.84[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	0.80[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	0.86[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];0.94[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.89[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];0.85[EUR][1000 genomes]
rs6955490	1.00[CEU][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.81[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6956305	0.84[ASN][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]
rs6976017	0.84[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];0.83[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]
rs73713580	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	0.83[MEX][hapmap]

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	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	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
rs2003499	OR2AE1	cis	parietal	SCAN
rs2003499	GATS	cis	parietal	SCAN
rs2003499	PILRB	cis	lymphoblastoid	GTEx
rs2003499	ZKSCAN1	cis	parietal	SCAN
rs2003499	CPSF4	cis	parietal	SCAN
rs2003499	STAG3	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99007200-99035400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr7:99007600-99015000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr7:99007800-99024000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr7:99008000-99018400	Strong transcription	Gastric	stomach
5	chr7:99008000-99018400	Strong transcription	Rectal Mucosa Donor 29	rectum
6	chr7:99008000-99019800	Weak transcription	Right Atrium	heart
7	chr7:99008000-99023400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
8	chr7:99008000-99023600	Strong transcription	HUES48 Cell Line	embryonic stem cell
9	chr7:99008000-99023800	Strong transcription	H1 Cell Line	embryonic stem cell
10	chr7:99008000-99023800	Strong transcription	Placenta	Placenta
11	chr7:99008000-99024000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr7:99008000-99024000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr7:99008000-99024000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr7:99008000-99024000	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr7:99008000-99024000	Strong transcription	Spleen	Spleen
16	chr7:99008000-99024200	Strong transcription	Primary monocytes fromperipheralblood	blood
17	chr7:99008000-99024200	Strong transcription	Fetal Stomach	stomach
18	chr7:99008000-99026600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr7:99008200-99023400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
20	chr7:99008200-99023600	Strong transcription	Fetal Intestine Large	intestine
21	chr7:99008200-99023800	Strong transcription	Cortex derived primary cultured neurospheres	brain
22	chr7:99008200-99023800	Strong transcription	Fetal Brain Female	brain
23	chr7:99008200-99023800	Strong transcription	Fetal Muscle Trunk	muscle
24	chr7:99008200-99023800	Strong transcription	Fetal Muscle Leg	muscle
25	chr7:99008200-99024000	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr7:99008200-99024000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
27	chr7:99008200-99024000	Strong transcription	Lung	lung
28	chr7:99008200-99024200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr7:99008400-99015000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr7:99008400-99015600	Strong transcription	Fetal Kidney	kidney
31	chr7:99008400-99015800	Strong transcription	Primary B cells from cord blood	blood
32	chr7:99008400-99016800	Strong transcription	Thymus	Thymus
33	chr7:99008400-99018800	Strong transcription	Fetal Lung	lung
34	chr7:99008400-99018800	Strong transcription	Rectal Mucosa Donor 31	rectum
35	chr7:99008400-99019000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr7:99008400-99019000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr7:99008400-99019000	Strong transcription	Stomach Smooth Muscle	stomach
38	chr7:99008400-99019200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr7:99008400-99019400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr7:99008400-99023200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr7:99008400-99023400	Strong transcription	Fetal Thymus	thymus
42	chr7:99008400-99023600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr7:99008400-99023600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr7:99008400-99023600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr7:99008400-99023600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr7:99008400-99023800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr7:99008400-99023800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr7:99008400-99024000	Strong transcription	Skeletal Muscle Female	skeletal muscle
49	chr7:99008600-99015400	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr7:99008600-99016000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links