Variant report

Variant	rs7218938
Chromosome Location	chr17:38501843-38501844
allele	C/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	MAX	chr17:38501192-38502028	SK-N-SH	brain:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
2	RCOR1	chr17:38501395-38502262	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:38501612-38502310	HepG2	liver:	n/a	n/a
4	POLR2A	chr17:38501736-38502007	HCT-116	colon:	n/a	n/a
5	EP300	chr17:38501211-38502596	HepG2	liver:	n/a	chr17:38501773-38501782 chr17:38501683-38501692 chr17:38501604-38501620
6	POLR2A	chr17:38501344-38502289	HepG2	liver:	n/a	n/a
7	E2F6	chr17:38501061-38502021	A549	lung:	n/a	chr17:38501634-38501644 chr17:38501122-38501133
8	ZEB1	chr17:38500572-38502778	HepG2	liver:	n/a	n/a
9	MAX	chr17:38501149-38502164	ECC-1	luminal epithelium:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
10	TEAD4	chr17:38501105-38502037	SK-N-SH	brain:	n/a	n/a
11	HNF4A	chr17:38501690-38502659	HepG2	liver:	n/a	chr17:38502182-38502196 chr17:38502182-38502197 chr17:38502423-38502435 chr17:38502182-38502195 chr17:38502178-38502200 chr17:38501880-38501893 chr17:38502183-38502195 chr17:38502182-38502196 chr17:38501880-38501893 chr17:38502182-38502196 chr17:38502183-38502196 chr17:38502180-38502198 chr17:38502422-38502430 chr17:38502135-38502143 chr17:38502181-38502196 chr17:38502183-38502195
12	HDAC2	chr17:38501211-38502487	HepG2	liver:	n/a	n/a
13	POLR2A	chr17:38501517-38502062	A549	lung:	n/a	n/a
14	CREB1	chr17:38501552-38502027	A549	lung:	n/a	n/a
15	POLR2A	chr17:38501412-38502110	ECC-1	luminal epithelium:	n/a	n/a
16	MYC	chr17:38501831-38501960	HepG2	liver:	n/a	n/a
17	MYC	chr17:38501242-38502047	K562	blood:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
18	MBD4	chr17:38501707-38502368	HepG2	liver:	n/a	n/a
19	TCF12	chr17:38500638-38502511	A549	lung:	n/a	chr17:38501639-38501646
20	POLR2A	chr17:38501562-38507336	MCF-7	breast:	n/a	n/a
21	JUND	chr17:38501314-38502091	A549	lung:	n/a	chr17:38501774-38501783
22	ELF1	chr17:38501661-38502085	HepG2	liver:	n/a	n/a
23	FOXP2	chr17:38501608-38501864	SK-N-MC	brain:	n/a	n/a
24	RAD21	chr17:38501490-38501965	SK-N-SH_RA	brain:	n/a	n/a
25	MAX	chr17:38501131-38502160	K562	blood:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
26	POLR2A	chr17:38501131-38502074	PANC-1	pancreas:	n/a	n/a
27	SIN3AK20	chr17:38501598-38502154	HepG2	liver:	n/a	n/a
28	MYC	chr17:38501231-38501977	K562	blood:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
29	EBF1	chr17:38501641-38501932	GM12878	blood:	n/a	n/a
30	TCF12	chr17:38501098-38502240	ECC-1	luminal epithelium:	n/a	chr17:38501639-38501646
31	GATA3	chr17:38501102-38502012	SK-N-SH	brain:	n/a	n/a
32	POLR2A	chr17:38501249-38501913	H1-neurons	neurons:	n/a	n/a
33	FOXA1	chr17:38501757-38502626	HepG2	liver:	n/a	n/a
34	ZBTB7A	chr17:38500512-38502170	ECC-1	luminal epithelium:	n/a	chr17:38501670-38501678
35	MAX	chr17:38501273-38501991	K562	blood:	n/a	chr17:38501439-38501449 chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
36	HNF4A	chr17:38501695-38502617	HepG2	liver:	n/a	chr17:38502182-38502196 chr17:38502182-38502197 chr17:38502423-38502435 chr17:38502182-38502195 chr17:38502178-38502200 chr17:38501880-38501893 chr17:38502183-38502195 chr17:38502182-38502196 chr17:38501880-38501893 chr17:38502182-38502196 chr17:38502183-38502196 chr17:38502180-38502198 chr17:38502422-38502430 chr17:38502135-38502143 chr17:38502181-38502196 chr17:38502183-38502195
37	NFIC	chr17:38501216-38502287	ECC-1	luminal epithelium:	n/a	n/a
38	UBTF	chr17:38501367-38502089	K562	blood:	n/a	n/a
39	EP300	chr17:38501084-38502116	ECC-1	luminal epithelium:	n/a	chr17:38501773-38501782 chr17:38501683-38501692 chr17:38501604-38501620
40	TEAD4	chr17:38501150-38502263	ECC-1	luminal epithelium:	n/a	n/a
41	MXI1	chr17:38496997-38502710	SK-N-SH	brain:	n/a	chr17:38502219-38502234
42	EGR1	chr17:38501285-38502003	K562	blood:	n/a	chr17:38501581-38501596 chr17:38501582-38501595 chr17:38501663-38501673 chr17:38501777-38501787
43	IRF1	chr17:38501832-38501892	K562	blood:	n/a	n/a
44	MAZ	chr17:38501270-38502129	K562	blood:	n/a	chr17:38501440-38501451 chr17:38501442-38501449 chr17:38501801-38501811 chr17:38501664-38501674 chr17:38501441-38501450 chr17:38501440-38501450
45	POLR2A	chr17:38501052-38502090	SK-N-SH	brain:	n/a	n/a
46	HNF4G	chr17:38501598-38502651	HepG2	liver:	n/a	chr17:38502115-38502130 chr17:38502182-38502196 chr17:38502182-38502197 chr17:38502423-38502435 chr17:38502182-38502195 chr17:38502178-38502200 chr17:38501880-38501893 chr17:38502183-38502195 chr17:38502182-38502196 chr17:38501880-38501893 chr17:38502182-38502196 chr17:38502183-38502196 chr17:38502180-38502198 chr17:38502422-38502430 chr17:38502135-38502143 chr17:38502183-38502195
47	POLR2A	chr17:38501206-38502094	PFSK-1	brain:	n/a	n/a
48	POLR2A	chr17:38501444-38502428	HepG2	liver:	n/a	n/a
49	ELF1	chr17:38501659-38502199	A549	lung:	n/a	n/a
50	POLR2A	chr17:38501093-38502040	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:38472788..38480698-chr17:38493295..38509406,39	K562	blood:
2	chr17:38464338..38472007-chr17:38495904..38503617,17	K562	blood:
3	chr17:38275824..38279709-chr17:38496937..38502326,5	K562	blood:
4	chr17:38458898..38461237-chr17:38499745..38502287,2	K562	blood:

Variant related genes	Relation type
ENSG00000265666	TF binding region
ENSG00000188895	Chromatin interaction
ENSG00000270145	Chromatin interaction
ENSG00000131759	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1130199	0.83[YRI][hapmap];0.90[AMR][1000 genomes]
rs12936565	0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12937995	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12944531	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12947188	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs34789145	0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7213066	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs7224658	0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8065665	0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs8067148	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8072718	0.93[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8074251	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8076915	0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs9892367	0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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
2	nsv833445	chr17:38466474-38637969	Flanking Active TSS Enhancers Bivalent/Poised TSS Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1057471	chr17:38467043-38502453	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
4	nsv1058540	chr17:38467043-38515087	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7218938	RAPGEFL1	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38497000-38502400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
2	chr17:38497400-38502000	Active TSS	Pancreatic Islets	Pancreatic Islet
3	chr17:38497400-38502200	Active TSS	Fetal Kidney	kidney
4	chr17:38497600-38502000	Active TSS	HSMMtube	muscle
5	chr17:38497600-38502200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
6	chr17:38498000-38508000	Weak transcription	Dnd41	blood
7	chr17:38498200-38507200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:38498400-38502400	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr17:38498600-38502400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
10	chr17:38498600-38502600	Flanking Active TSS	Primary hematopoietic stem cells	blood
11	chr17:38498600-38502600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr17:38498600-38503000	Flanking Active TSS	Fetal Muscle Trunk	muscle
13	chr17:38498600-38505800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr17:38498800-38502400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr17:38498800-38502400	Flanking Active TSS	Osteobl	bone
16	chr17:38498800-38502600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
17	chr17:38498800-38502600	Flanking Active TSS	Adipose Nuclei	Adipose
18	chr17:38498800-38502600	Flanking Active TSS	Fetal Brain Female	brain
19	chr17:38498800-38502600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
20	chr17:38499000-38502400	Flanking Active TSS	Primary T cells from cord blood	blood
21	chr17:38499000-38502400	Flanking Active TSS	NH-A	brain
22	chr17:38499000-38502600	Flanking Active TSS	HUVEC	blood vessel
23	chr17:38499000-38502800	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr17:38499000-38504000	Flanking Active TSS	Stomach Smooth Muscle	stomach
25	chr17:38499400-38502400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr17:38499400-38502400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
27	chr17:38499400-38502400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr17:38499400-38502600	Transcr. at gene 5' and 3'	Primary neutrophils fromperipheralblood	blood
29	chr17:38499400-38502600	Flanking Active TSS	Liver	Liver
30	chr17:38499400-38503200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr17:38499600-38502600	Flanking Active TSS	Right Ventricle	heart
32	chr17:38500000-38507000	Enhancers	NHDF-Ad	bronchial
33	chr17:38500200-38502400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
34	chr17:38500400-38502000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
35	chr17:38500400-38502000	Flanking Active TSS	Spleen	Spleen
36	chr17:38500400-38502200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
37	chr17:38500400-38502200	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
38	chr17:38500400-38502400	Flanking Active TSS	Left Ventricle	heart
39	chr17:38500400-38502400	Flanking Active TSS	A549	lung
40	chr17:38500400-38502600	Flanking Active TSS	NHLF	lung
41	chr17:38500400-38502800	Flanking Active TSS	Colonic Mucosa	Colon
42	chr17:38500600-38502000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
43	chr17:38500600-38502200	Flanking Active TSS	Primary T cells fromperipheralblood	blood
44	chr17:38500600-38502200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
45	chr17:38500600-38502200	Flanking Active TSS	Lung	lung
46	chr17:38500600-38502200	Flanking Active TSS	Pancreas	Pancrea
47	chr17:38500600-38502200	Flanking Active TSS	Psoas Muscle	Psoas
48	chr17:38500600-38502600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr17:38500600-38502600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
50	chr17:38500600-38502600	Flanking Active TSS	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links