Variant report

Variant	rs9892367
Chromosome Location	chr17:38463388-38463389
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF7L2	chr17:38462904-38463451	HEK293	kidney:	n/a	chr17:38463288-38463298 chr17:38463287-38463296 chr17:38462976-38462986 chr17:38463284-38463300 chr17:38463284-38463300 chr17:38462976-38462985 chr17:38463285-38463299
2	CTCF	chr17:38463240-38463390	AG09309	skin:	n/a	n/a
3	MAZ	chr17:38463288-38463674	Hela-S3	cervix:	n/a	n/a
4	SIN3AK20	chr17:38463280-38463581	SK-N-SH	brain:	n/a	n/a
5	MAZ	chr17:38463209-38463731	K562	blood:	n/a	n/a
6	FOSL2	chr17:38463076-38464189	SK-N-SH	brain:	n/a	n/a
7	MAFF	chr17:38463120-38463515	HepG2	liver:	n/a	chr17:38463326-38463344
8	POLR2A	chr17:38462575-38464042	ECC-1	luminal epithelium:	n/a	n/a
9	TEAD4	chr17:38463041-38463869	K562	blood:	n/a	n/a
10	TFAP2A	chr17:38462667-38463986	Hela-S3	cervix:	n/a	chr17:38463158-38463169 chr17:38463158-38463169 chr17:38463158-38463169 chr17:38463158-38463169 chr17:38463566-38463581 chr17:38463564-38463579
11	MAFK	chr17:38463143-38463537	HepG2	liver:	n/a	chr17:38463331-38463342 chr17:38463327-38463343 chr17:38463327-38463342 chr17:38463330-38463344
12	CTCF	chr17:38463362-38463417	MCF-7	breast:	n/a	n/a
13	POLR2A	chr17:38463122-38464141	SK-N-SH	brain:	n/a	n/a
14	GATA3	chr17:38463201-38463693	T-47D	breast:	n/a	chr17:38463601-38463608 chr17:38463447-38463455
15	ZBTB33	chr17:38463226-38464144	SK-N-SH	brain:	n/a	n/a
16	POLR2A	chr17:38462499-38466013	PANC-1	pancreas:	n/a	n/a
17	POLR2A	chr17:38463268-38463466	H1-hESC	embryonic stem cell:	n/a	n/a
18	TCF7L2	chr17:38462613-38464381	PANC-1	pancreas:	n/a	chr17:38463288-38463298 chr17:38463287-38463296 chr17:38462976-38462986 chr17:38463284-38463300 chr17:38463284-38463300 chr17:38462976-38462985 chr17:38463285-38463299
19	EP300	chr17:38463312-38463752	T-47D	breast:	n/a	n/a
20	GATA3	chr17:38463191-38463748	T-47D	breast:	n/a	chr17:38463601-38463608 chr17:38463447-38463455
21	GATA2	chr17:38462667-38464127	SH-SY5Y	brain:	n/a	chr17:38462872-38462879 chr17:38463601-38463608 chr17:38463034-38463041 chr17:38462872-38462879 chr17:38463032-38463041 chr17:38462872-38462879 chr17:38463030-38463043
22	ZBTB7A	chr17:38463244-38463919	K562	blood:	n/a	n/a
23	SIN3AK20	chr17:38463165-38464025	SK-N-SH	brain:	n/a	n/a
24	MYC	chr17:38463272-38463534	K562	blood:	n/a	n/a
25	POLR2A	chr17:38462539-38464322	MCF-7	breast:	n/a	n/a
26	PBX3	chr17:38463088-38464186	SK-N-SH	brain:	n/a	n/a
27	JUND	chr17:38463102-38464151	SK-N-SH	brain:	n/a	n/a
28	POLR2A	chr17:38462183-38465766	HepG2	liver:	n/a	n/a
29	RCOR1	chr17:38463276-38463669	K562	blood:	n/a	n/a
30	POLR2A	chr17:38462453-38464605	PFSK-1	brain:	n/a	n/a
31	NR2F2	chr17:38463135-38464479	MCF-7	breast:	n/a	n/a
32	MEF2A	chr17:38463136-38464194	SK-N-SH	brain:	n/a	n/a
33	EP300	chr17:38463306-38463681	T-47D	breast:	n/a	n/a
34	PBX3	chr17:38463101-38464237	SK-N-SH	brain:	n/a	n/a
35	GATA3	chr17:38463180-38463864	MCF-7	breast:	n/a	chr17:38463601-38463608 chr17:38463447-38463455
36	NFATC1	chr17:38462933-38464070	GM12878	blood:	n/a	n/a
37	POLR2A	chr17:38463189-38463750	K562	blood:	n/a	n/a
38	HMGN3	chr17:38463296-38463525	K562	blood:	n/a	n/a
39	MAX	chr17:38463139-38463666	SK-N-SH	brain:	n/a	n/a
40	POLR2A	chr17:38462257-38464316	H1-hESC	embryonic stem cell:	n/a	n/a
41	CTCF	chr17:38463300-38463450	AG04449	skin:	n/a	n/a
42	JUND	chr17:38463359-38463665	K562	blood:	n/a	n/a
43	CTCF	chr17:38463260-38463410	NHEK	skin:	n/a	n/a
44	RAD21	chr17:38463172-38463660	SK-N-SH_RA	brain:	n/a	chr17:38463368-38463380
45	UBTF	chr17:38463305-38463608	K562	blood:	n/a	n/a
46	EP300	chr17:38463253-38463708	MCF-7	breast:	n/a	chr17:38463279-38463292
47	KAP1	chr17:38462652-38464428	HEK293	kidney:	n/a	n/a
48	EP300	chr17:38463127-38464055	SK-N-SH_RA	brain:	n/a	chr17:38463279-38463292
49	TCF7L2	chr17:38462652-38463518	MCF-7	breast:	n/a	chr17:38463288-38463298 chr17:38463287-38463296 chr17:38462976-38462986 chr17:38463284-38463300 chr17:38463284-38463300 chr17:38462976-38462985 chr17:38463285-38463299
50	CTCF	chr17:38463280-38463430	AG09319	gingival:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38461366..38465134-chr17:38511894..38515079,3	K562	blood:
2	chr17:38463050..38463710-chr17:38478439..38479155,2	MCF-7	breast:
3	chr17:38351055..38353066-chr17:38461738..38464698,2	K562	blood:
4	chr17:38462607..38464232-chr17:38573355..38574958,2	K562	blood:
5	chr17:38331368..38338782-chr17:38460574..38470405,11	MCF-7	breast:
6	chr17:38461615..38484404-chr17:38597525..38608992,85	MCF-7	breast:
7	chr17:38462430..38464152-chr17:38482291..38484483,2	K562	blood:

Variant related genes	Relation type
RARA	TF binding region
ENSG00000141753	Chromatin interaction
ENSG00000131747	Chromatin interaction
ENSG00000108352	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1130199	1.00[ASW][hapmap];0.98[LWK][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12936565	0.92[ASW][hapmap];0.89[LWK][hapmap];0.81[MKK][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes]
rs12937995	0.92[ASW][hapmap];0.94[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs12944531	0.83[AFR][1000 genomes]
rs12947188	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs34789145	0.92[ASW][hapmap];0.91[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap];0.86[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7213066	0.85[AFR][1000 genomes]
rs7218938	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs7224658	0.92[ASW][hapmap];0.89[LWK][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8065665	0.92[ASW][hapmap];0.88[LWK][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]
rs8067148	0.81[AFR][1000 genomes]
rs8072718	0.89[YRI][hapmap];0.82[AFR][1000 genomes]
rs8074251	0.81[AFR][1000 genomes]
rs8076915	0.92[ASW][hapmap];0.92[LWK][hapmap];0.81[MKK][hapmap];0.86[YRI][hapmap]

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	nsv1058194	chr17:38457226-38502453	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9892367	RAPGEFL1	cis	multi-tissue	Pritchard
rs9892367	RAPGEFL1	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38459000-38465400	Enhancers	Fetal Muscle Leg	muscle
2	chr17:38459000-38465400	Enhancers	Fetal Stomach	stomach
3	chr17:38459200-38465200	Enhancers	Fetal Intestine Large	intestine
4	chr17:38459200-38465400	Enhancers	Cortex derived primary cultured neurospheres	brain
5	chr17:38459200-38473800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr17:38459600-38465200	Enhancers	Placenta	Placenta
7	chr17:38460000-38463400	Weak transcription	Primary B cells from cord blood	blood
8	chr17:38460000-38463400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr17:38460000-38464000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:38460000-38465200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr17:38460000-38465200	Weak transcription	Brain Angular Gyrus	brain
12	chr17:38460200-38463600	Weak transcription	Right Ventricle	heart
13	chr17:38460200-38464000	Weak transcription	Brain Hippocampus Middle	brain
14	chr17:38460400-38463400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr17:38460600-38463400	Weak transcription	Left Ventricle	heart
16	chr17:38460600-38463600	Weak transcription	Brain Substantia Nigra	brain
17	chr17:38460600-38463800	Weak transcription	Brain Cingulate Gyrus	brain
18	chr17:38460800-38465000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr17:38461000-38465200	Enhancers	Fetal Thymus	thymus
20	chr17:38461400-38465000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr17:38461600-38465000	Enhancers	H1 Cell Line	embryonic stem cell
22	chr17:38461800-38465000	Enhancers	Fetal Intestine Small	intestine
23	chr17:38461800-38465400	Enhancers	Breast Myoepithelial Primary Cells	Breast
24	chr17:38461800-38466600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
25	chr17:38462200-38466800	Enhancers	NHLF	lung
26	chr17:38462200-38473200	Enhancers	NHDF-Ad	bronchial
27	chr17:38462400-38464200	Enhancers	Primary T cells from cord blood	blood
28	chr17:38462400-38465000	Enhancers	HepG2	liver
29	chr17:38462400-38465200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr17:38462400-38465200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
31	chr17:38462400-38465200	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr17:38462400-38465200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr17:38462400-38465200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr17:38462400-38465200	Enhancers	Fetal Heart	heart
35	chr17:38462400-38465400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr17:38462400-38468800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
37	chr17:38462600-38463400	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr17:38462600-38463400	Enhancers	HSMM	muscle
39	chr17:38462600-38463600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:38462600-38463600	Flanking Active TSS	Duodenum Mucosa	Duodenum
41	chr17:38462600-38463800	Flanking Active TSS	Osteobl	bone
42	chr17:38462600-38464000	Enhancers	HMEC	breast
43	chr17:38462600-38464000	Enhancers	NHEK	skin
44	chr17:38462600-38464200	Enhancers	Adipose Nuclei	Adipose
45	chr17:38462600-38464400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr17:38462600-38464600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
47	chr17:38462600-38464600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr17:38462600-38464600	Enhancers	Colon Smooth Muscle	Colon
49	chr17:38462600-38464600	Enhancers	Fetal Kidney	kidney
50	chr17:38462600-38464600	Enhancers	Fetal Muscle Trunk	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links