Variant report

Variant	rs17118403
Chromosome Location	chr12:56630067-56630068
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:21)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:21 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr12:56630005-56630584	A549	lung:	n/a	n/a
2	POLR2A	chr12:56629799-56631302	PFSK-1	brain:	n/a	n/a
3	POLR2A	chr12:56629846-56631078	ECC-1	luminal epithelium:	n/a	n/a
4	POLR2A	chr12:56629885-56630672	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr12:56628235-56634072	HepG2	liver:	n/a	n/a
6	POLR2A	chr12:56630037-56630090	Hela-S3	cervix:	n/a	n/a
7	POLR2A	chr12:56629838-56631376	SK-N-MC	brain:	n/a	n/a
8	POLR2A	chr12:56629842-56631446	K562	blood:	n/a	n/a
9	POLR2A	chr12:56629704-56631243	U87	brain:	n/a	n/a
10	POLR2A	chr12:56629998-56631282	SK-N-SH	brain:	n/a	n/a
11	POLR2A	chr12:56629711-56631163	GM12892	blood:	n/a	n/a
12	PBX3	chr12:56629996-56630860	A549	lung:	n/a	n/a
13	POLR2A	chr12:56629916-56631203	GM12892	blood:	n/a	n/a
14	POLR2A	chr12:56629976-56630121	H1-hESC	embryonic stem cell:	n/a	n/a
15	POLR2A	chr12:56629970-56630132	ProgFib	skin:	n/a	n/a
16	BCL3	chr12:56629848-56631188	A549	lung:	n/a	n/a
17	POLR2A	chr12:56629699-56631443	U87	brain:	n/a	n/a
18	POLR2A	chr12:56629734-56631243	U87	brain:	n/a	n/a
19	POLR2A	chr12:56629743-56632318	HepG2	liver:	n/a	n/a
20	POLR2A	chr12:56629946-56631027	MCF-7	breast:	n/a	n/a
21	POLR2A	chr12:56629645-56632297	U87	brain:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr12:56625950..56631814-chr12:56649549..56655223,8	MCF-7	breast:
2	chr12:56614288..56617250-chr12:56628916..56630497,2	K562	blood:
3	chr12:56514942..56516725-chr12:56628442..56630257,2	K562	blood:
4	chr12:56622689..56625267-chr12:56629999..56633597,3	MCF-7	breast:
5	chr12:56510354..56511965-chr12:56629667..56631737,2	K562	blood:

No data

Variant related genes	Relation type
SLC39A5	TF binding region
ENSG00000229117	Chromatin interaction
ENSG00000139540	Chromatin interaction
ENSG00000135482	Chromatin interaction
ENSG00000139579	Chromatin interaction
ENSG00000139645	Chromatin interaction
ENSG00000181852	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10876882	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap]
rs11171803	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11171806	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11575224	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11575229	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11575231	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11575232	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs11575234	0.82[ASN][1000 genomes]
rs11575248	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1274490	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1274493	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1274496	0.86[EUR][1000 genomes]
rs1295772	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118409	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17118431	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17118439	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1802236	1.00[AFR][1000 genomes]
rs2020854	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];0.93[TSI][hapmap];0.87[ASN][1000 genomes]
rs2066807	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2066808	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs2066818	0.89[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs2066819	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.82[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2291361	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2306693	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2306694	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2371454	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2371494	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs2629447	0.89[CEU][hapmap];0.91[ASN][1000 genomes]
rs2629452	0.84[EUR][1000 genomes]
rs2643623	0.84[ASN][1000 genomes]
rs2643626	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs2695782	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs2695788	0.91[ASN][1000 genomes]
rs2695789	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs35526714	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs41363748	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[MEX][hapmap];0.87[TSI][hapmap]
rs41392645	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.93[TSI][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs41423244	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57137641	1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs57279772	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs57343616	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57367440	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs57870697	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs58852079	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59295315	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59626664	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59811639	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59822547	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59917308	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60192809	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60542959	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60913149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs703830	0.91[ASN][1000 genomes]
rs744051	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773652	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs773664	0.91[ASN][1000 genomes]
rs773665	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[ASN][1000 genomes]
rs808919	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs871130	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[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	nsv1043622	chr12:56571476-56974448	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases
2	nsv541500	chr12:56571476-56974448	Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17118403	RP11-977G19.11	cis	Artery Tibial	GTEx
rs17118403	RP11-977G19.11	cis	Artery Aorta	GTEx
rs17118403	TMEM4	Cis_1M	lymphoblastoid	RTeQTL
rs17118403	RPS26	cis	lymphoblastoid	seeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:56618600-56633800	Weak transcription	Aorta	Aorta
2	chr12:56618800-56630200	Weak transcription	Ovary	ovary
3	chr12:56618800-56630400	Weak transcription	Fetal Thymus	thymus
4	chr12:56618800-56631200	Weak transcription	HSMMtube	muscle
5	chr12:56618800-56633000	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr12:56618800-56633000	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:56618800-56634600	Weak transcription	Psoas Muscle	Psoas
8	chr12:56618800-56635200	Weak transcription	Small Intestine	intestine
9	chr12:56618800-56635400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr12:56618800-56637800	Weak transcription	Fetal Kidney	kidney
11	chr12:56619000-56630400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr12:56619000-56631000	Weak transcription	Primary B cells from peripheral blood	blood
13	chr12:56619000-56632000	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:56619000-56633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr12:56619000-56633200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:56619000-56633400	Weak transcription	HUES6 Cell Line	embryonic stem cell
17	chr12:56619000-56633600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr12:56619000-56634000	Weak transcription	Primary B cells from cord blood	blood
19	chr12:56619000-56634800	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr12:56619200-56630400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr12:56619200-56631000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr12:56619200-56631200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr12:56619200-56631400	Weak transcription	Brain Cingulate Gyrus	brain
24	chr12:56619200-56632400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr12:56619200-56633000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:56619200-56633000	Weak transcription	Primary hematopoietic stem cells	blood
27	chr12:56619200-56633000	Weak transcription	Left Ventricle	heart
28	chr12:56619200-56633400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
29	chr12:56619200-56633400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:56619200-56634400	Weak transcription	Fetal Lung	lung
31	chr12:56619200-56634600	Weak transcription	HUVEC	blood vessel
32	chr12:56619200-56635000	Weak transcription	HSMM	muscle
33	chr12:56619200-56635400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
34	chr12:56619200-56637600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:56619400-56632600	Weak transcription	NHDF-Ad	bronchial
36	chr12:56619400-56634600	Weak transcription	NH-A	brain
37	chr12:56619400-56637200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
38	chr12:56619400-56637800	Weak transcription	Right Atrium	heart
39	chr12:56619600-56632600	Weak transcription	Primary T helper cells fromperipheralblood	blood
40	chr12:56619600-56634600	Weak transcription	HMEC	breast
41	chr12:56619600-56635600	Weak transcription	GM12878-XiMat	blood
42	chr12:56619600-56638000	Weak transcription	Hela-S3	cervix
43	chr12:56619800-56638800	Weak transcription	Fetal Brain Male	brain
44	chr12:56620200-56631800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:56620200-56633800	Weak transcription	Brain Substantia Nigra	brain
46	chr12:56621600-56630200	Weak transcription	Adipose Nuclei	Adipose
47	chr12:56621600-56632200	Weak transcription	Brain Inferior Temporal Lobe	brain
48	chr12:56621600-56633000	Weak transcription	HUES48 Cell Line	embryonic stem cell
49	chr12:56621600-56633000	Weak transcription	Skeletal Muscle Female	skeletal muscle
50	chr12:56623200-56630400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links