Variant report

Variant	rs5998114
Chromosome Location	chr22:32151214-32151215
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:6)
CpG islands
(count:0)
Chromatin interactive
region (count:14)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:6 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	ESRRA	chr22:32148093-32151618	GM12878	blood:	n/a	n/a
2	POLR2A	chr22:32148838-32151230	HepG2	liver:	n/a	n/a
3	RUNX3	chr22:32149312-32151231	GM12878	blood:	n/a	chr22:32150378-32150387
4	POLR2A	chr22:32151070-32151265	MCF10A-Er-Src	breast:	n/a	n/a
5	POLR2A	chr22:32151136-32151309	MCF10A-Er-Src	breast:	n/a	n/a
6	ARID3A	chr22:32151067-32151365	K562	blood:	n/a	n/a

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr22:32025067..32026955-chr22:32148287..32151224,2	K562	blood:
2	22:32053085-32061138..22:32150875-32154575	GM12878	blood:
3	22:32150875-32154575..22:32228866-32235273	GM12878	blood:
4	22:32150875-32154575..22:32162110-32166713	GM12878	blood:
5	22:32150875-32154575..22:32915608-32918105	GM12878	blood:
6	chr22:31363553..31366522-chr22:32148342..32151239,2	K562	blood:
7	22:32150875-32154575..22:32338420-32342898	K562	blood:
8	chr22:32148601..32151339-chr22:32339160..32341973,3	MCF-7	breast:
9	chr22:32148473..32152307-chr22:32339145..32342092,6	K562	blood:
10	22:32150875-32154575..22:32860159-32865649	GM12878	blood:
11	chr22:32149264..32152111-chr22:32339608..32342388,3	MCF-7	breast:
12	chr22:32147800..32152307-chr22:32338859..32342135,7	K562	blood:
13	chr22:32148657..32151429-chr22:32161601..32165600,4	MCF-7	breast:
14	22:32150875-32154575..22:32264718-32278135	GM12878	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SFI1-4	chr22:32150848-32151497	NONHSAT084913

No data

Variant related genes	Relation type
RN7SL20P	TF binding region
ENSG00000133422	Chromatin interaction
ENSG00000252909	Chromatin interaction
ENSG00000241878	Chromatin interaction
ENSG00000128254	Chromatin interaction
ENSG00000128245	Chromatin interaction
ENSG00000184459	Chromatin interaction
ENSG00000185666	Chromatin interaction
ENSG00000100150	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs1013703	0.90[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1076674	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.80[ASN][1000 genomes]
rs11089530	0.93[ASN][1000 genomes]
rs11089531	0.83[CEU][hapmap]
rs11703040	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11703079	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs11703102	1.00[CHB][hapmap]
rs11703104	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11703232	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs11703275	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs11703810	0.93[ASN][1000 genomes]
rs11703854	0.93[ASN][1000 genomes]
rs11704129	1.00[CHB][hapmap]
rs11704362	1.00[ASN][1000 genomes]
rs11704377	0.93[ASN][1000 genomes]
rs11705097	0.93[ASN][1000 genomes]
rs11705235	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs11705329	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs12157427	0.80[ASN][1000 genomes]
rs12157989	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12158002	1.00[CHB][hapmap]
rs12159673	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs12160120	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs12160737	0.80[ASN][1000 genomes]
rs12166848	0.80[ASN][1000 genomes]
rs131222	0.93[ASN][1000 genomes]
rs131224	0.93[ASN][1000 genomes]
rs131226	0.93[ASN][1000 genomes]
rs131228	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs131231	0.84[MEX][hapmap]
rs131235	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs131237	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs131241	1.00[ASN][1000 genomes]
rs131243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];1.00[ASN][1000 genomes]
rs131246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs131251	1.00[ASN][1000 genomes]
rs131252	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs131254	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap];0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs140079	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs140083	1.00[ASN][1000 genomes]
rs140085	1.00[ASN][1000 genomes]
rs16989291	0.92[MEX][hapmap]
rs16989374	1.00[CHB][hapmap];0.92[MEX][hapmap]
rs16989529	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs16989540	0.92[MEX][hapmap]
rs16989600	0.92[MEX][hapmap]
rs16989601	0.91[MEX][hapmap]
rs2040981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.87[ASN][1000 genomes]
rs2051583	0.92[MEX][hapmap]
rs2413058	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs3804088	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.80[ASN][1000 genomes]
rs4603881	0.82[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs55645350	0.93[ASN][1000 genomes]
rs55699591	0.93[ASN][1000 genomes]
rs5753753	0.80[ASN][1000 genomes]
rs5994417	1.00[CHB][hapmap]
rs5994424	0.93[ASN][1000 genomes]
rs5994436	0.83[CEU][hapmap]
rs5998066	1.00[CHB][hapmap]
rs5998068	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap]
rs5998074	0.84[MEX][hapmap]
rs5998079	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs5998080	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs5998081	0.80[ASN][1000 genomes]
rs5998084	0.80[ASN][1000 genomes]
rs5998085	1.00[CHB][hapmap]
rs5998089	0.80[ASN][1000 genomes]
rs5998091	0.80[ASN][1000 genomes]
rs5998093	0.93[ASN][1000 genomes]
rs5998095	0.93[ASN][1000 genomes]
rs5998098	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.93[ASN][1000 genomes]
rs5998099	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs5998103	0.93[ASN][1000 genomes]
rs5998113	1.00[ASN][1000 genomes]
rs5998115	0.92[MEX][hapmap];0.86[MKK][hapmap]
rs5998116	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5998123	0.93[ASN][1000 genomes]
rs5998133	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.84[MEX][hapmap];0.93[ASN][1000 genomes]
rs5998134	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[ASN][1000 genomes]
rs5998135	0.91[CEU][hapmap];1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs5998144	0.92[MEX][hapmap]
rs5998173	1.00[JPT][hapmap]
rs60136719	0.93[ASN][1000 genomes]
rs60209974	0.80[ASN][1000 genomes]
rs60669705	0.93[ASN][1000 genomes]
rs61273982	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62238893	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs62238895	0.93[ASN][1000 genomes]
rs62238904	0.93[ASN][1000 genomes]
rs62238906	0.93[ASN][1000 genomes]
rs62239186	0.80[ASN][1000 genomes]
rs62239187	0.80[ASN][1000 genomes]
rs62239188	0.80[ASN][1000 genomes]
rs62240515	1.00[ASN][1000 genomes]
rs62240684	0.93[ASN][1000 genomes]
rs62240686	0.93[ASN][1000 genomes]
rs62240687	0.93[ASN][1000 genomes]
rs7289259	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7289535	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7289702	0.83[CEU][hapmap]
rs7291898	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73162139	1.00[ASN][1000 genomes]
rs740227	0.93[ASN][1000 genomes]
rs8136047	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs8141719	1.00[CHB][hapmap];0.93[ASN][1000 genomes]
rs8143084	0.80[ASN][1000 genomes]
rs81946	0.93[ASN][1000 genomes]
rs9619222	0.80[ASN][1000 genomes]
rs9619224	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs9621316	0.80[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1060929	chr22:32102701-32176860	Flanking Active TSS Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs5998114	INPP5J	cis	parietal	SCAN
rs5998114	SEZ6L	cis	cerebellum	SCAN
rs5998114	SELM	cis	cerebellum	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr22:32150200-32151400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
2	chr22:32150200-32151400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr22:32150200-32151400	Flanking Active TSS	Fetal Heart	heart
4	chr22:32150200-32151400	Flanking Active TSS	Dnd41	blood
5	chr22:32150200-32151400	Flanking Active TSS	HMEC	breast
6	chr22:32150200-32151400	Flanking Active TSS	NHEK	skin
7	chr22:32150200-32151600	Flanking Active TSS	Liver	Liver
8	chr22:32150400-32151400	Flanking Active TSS	A549	lung
9	chr22:32150400-32151400	Flanking Active TSS	K562	blood
10	chr22:32150400-32154400	Weak transcription	Ovary	ovary
11	chr22:32150400-32161200	Weak transcription	Aorta	Aorta
12	chr22:32150400-32174200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr22:32150600-32151400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr22:32150600-32151400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr22:32150600-32151400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr22:32150600-32151400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr22:32150600-32151400	Flanking Active TSS	Pancreatic Islets	Pancreatic Islet
18	chr22:32150600-32151800	Flanking Active TSS	GM12878-XiMat	blood
19	chr22:32150600-32154400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr22:32150600-32172600	Weak transcription	Small Intestine	intestine
21	chr22:32150800-32151400	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr22:32150800-32151400	Enhancers	Primary T cells from cord blood	blood
23	chr22:32150800-32151400	Enhancers	Primary T killer memory cells from peripheral blood	blood
24	chr22:32150800-32151400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr22:32150800-32151400	Enhancers	Fetal Brain Female	brain
26	chr22:32150800-32151600	Enhancers	HUVEC	blood vessel
27	chr22:32150800-32154000	Weak transcription	Fetal Muscle Trunk	muscle
28	chr22:32150800-32154200	Weak transcription	Gastric	stomach
29	chr22:32150800-32154200	Weak transcription	Left Ventricle	heart
30	chr22:32150800-32154200	Weak transcription	Right Ventricle	heart
31	chr22:32150800-32161000	Weak transcription	HSMMtube	muscle
32	chr22:32150800-32212800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr22:32151000-32151400	Enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr22:32151000-32151400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr22:32151000-32151400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr22:32151000-32151400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr22:32151000-32151400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
38	chr22:32151000-32151400	Enhancers	Brain Hippocampus Middle	brain
39	chr22:32151000-32151400	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr22:32151000-32151400	Active TSS	Fetal Brain Male	brain
41	chr22:32151000-32151600	Enhancers	Primary T helper cells PMA-I stimulated	--
42	chr22:32151000-32151600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr22:32151000-32151600	Enhancers	Sigmoid Colon	Sigmoid Colon
44	chr22:32151000-32151800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr22:32151000-32153200	Weak transcription	Esophagus	oesophagus
46	chr22:32151000-32153200	Weak transcription	Fetal Muscle Leg	muscle
47	chr22:32151000-32153800	Weak transcription	Colonic Mucosa	Colon
48	chr22:32151000-32154000	Weak transcription	Primary hematopoietic stem cells	blood
49	chr22:32151000-32154200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
50	chr22:32151000-32154200	Weak transcription	H9 Cell Line	embryonic stem cell

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