Variant report

Variant	rs7248780
Chromosome Location	chr19:38878033-38878034
allele	A/C
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	POLR2A	chr19:38878016-38879051	SK-N-MC	brain:	n/a	n/a
2	NR2F2	chr19:38877744-38878688	K562	blood:	n/a	n/a
3	GABPA	chr19:38877876-38878250	H1-hESC	embryonic stem cell:	n/a	n/a
4	ZMIZ1	chr19:38877893-38878145	K562	blood:	n/a	n/a
5	ELK1	chr19:38877987-38878186	K562	blood:	n/a	n/a
6	POLR2A	chr19:38871440-38886227	PFSK-1	brain:	n/a	n/a
7	CBX3	chr19:38877931-38878265	K562	blood:	n/a	n/a
8	JUND	chr19:38877950-38879614	A549	lung:	n/a	n/a
9	CUX1	chr19:38877967-38878158	K562	blood:	n/a	n/a
10	SP4	chr19:38877947-38879354	H1-hESC	embryonic stem cell:	n/a	chr19:38878702-38878718 chr19:38878247-38878263 chr19:38878006-38878022 chr19:38878722-38878738 chr19:38878567-38878583 chr19:38878676-38878687 chr19:38878548-38878564 chr19:38878704-38878715 chr19:38878915-38878931 chr19:38878722-38878733 chr19:38878546-38878562 chr19:38878747-38878763
11	SIN3A	chr19:38877933-38878443	H1-hESC	embryonic stem cell:	n/a	chr19:38878111-38878119
12	MAFK	chr19:38877976-38878227	K562	blood:	n/a	n/a
13	PBX3	chr19:38877935-38879409	A549	lung:	n/a	n/a
14	POLR2A	chr19:38877152-38881859	PFSK-1	brain:	n/a	n/a
15	POLR2A	chr19:38874785-38879102	A549	lung:	n/a	n/a
16	TEAD4	chr19:38877868-38878235	K562	blood:	n/a	n/a
17	ZNF263	chr19:38877980-38878461	HEK293-T-REx	kidney:	n/a	n/a
18	EP300	chr19:38877986-38878217	K562	blood:	n/a	n/a
19	POLR2A	chr19:38877960-38879248	SK-N-SH	brain:	n/a	n/a
20	POLR2A	chr19:38869603-38879135	K562	blood:	n/a	n/a
21	TCF12	chr19:38877896-38880448	A549	lung:	n/a	chr19:38878480-38878487
22	TEAD4	chr19:38877808-38878551	K562	blood:	n/a	n/a
23	POLR2A	chr19:38877558-38878783	ECC-1	luminal epithelium:	n/a	n/a
24	MAZ	chr19:38877673-38879268	K562	blood:	n/a	chr19:38878570-38878580 chr19:38878754-38878763 chr19:38878750-38878760
25	POLR2A	chr19:38877745-38879927	MCF10A-Er-Src	breast:	n/a	n/a
26	POLR2A	chr19:38877882-38878119	HUVEC	blood vessel:	n/a	n/a
27	MAX	chr19:38877977-38878337	K562	blood:	n/a	n/a
28	POLR2A	chr19:38877536-38878371	GM12892	blood:	n/a	n/a
29	POLR2A	chr19:38877956-38878886	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr19:38877808-38879269	U87	brain:	n/a	n/a
31	POLR2A	chr19:38873453-38879163	K562	blood:	n/a	n/a
32	PBX3	chr19:38877932-38879304	A549	lung:	n/a	n/a
33	ZBTB7A	chr19:38877661-38879283	K562	blood:	n/a	chr19:38878920-38878927
34	FOSL2	chr19:38877935-38879254	A549	lung:	n/a	n/a
35	SIN3AK20	chr19:38877902-38878564	A549	lung:	n/a	n/a
36	POLR2A	chr19:38873627-38879112	K562	blood:	n/a	n/a
37	ELF1	chr19:38877947-38879277	A549	lung:	n/a	n/a
38	TBL1XR1	chr19:38877993-38878158	K562	blood:	n/a	n/a
39	POLR2A	chr19:38877611-38878665	GM12878	blood:	n/a	n/a
40	POLR2A	chr19:38877979-38878329	GM12892	blood:	n/a	n/a
41	BHLHE40	chr19:38877875-38878197	K562	blood:	n/a	chr19:38878001-38878017
42	RCOR1	chr19:38877892-38878780	K562	blood:	n/a	n/a
43	HMGN3	chr19:38877286-38878075	K562	blood:	n/a	n/a
44	POLR2A	chr19:38877942-38878176	GM12878	blood:	n/a	n/a
45	MAX	chr19:38877849-38878491	ECC-1	luminal epithelium:	n/a	n/a
46	POLR2A	chr19:38877942-38878593	K562	blood:	n/a	n/a
47	POLR2A	chr19:38877802-38879275	U87	brain:	n/a	n/a
48	SP1	chr19:38877908-38879494	A549	lung:	n/a	chr19:38879469-38879478 chr19:38878247-38878259 chr19:38878009-38878019 chr19:38878549-38878558 chr19:38878549-38878559 chr19:38878803-38878815 chr19:38879464-38879478 chr19:38878804-38878813 chr19:38878571-38878580 chr19:38879019-38879029 chr19:38878915-38878927 chr19:38878010-38878019 chr19:38878247-38878259 chr19:38878750-38878760 chr19:38878704-38878716 chr19:38878989-38878999 chr19:38878803-38878815 chr19:38878222-38878231 chr19:38878009-38878018 chr19:38878676-38878687 chr19:38879467-38879479 chr19:38878915-38878927 chr19:38878569-38878581 chr19:38878704-38878716 chr19:38878704-38878715 chr19:38878570-38878579 chr19:38878723-38878732 chr19:38878804-38878814 chr19:38878749-38878761 chr19:38878705-38878719 chr19:38878750-38878760 chr19:38878569-38878581 chr19:38879018-38879030 chr19:38878548-38878560 chr19:38879018-38879030 chr19:38878804-38878818 chr19:38878749-38878761 chr19:38878804-38878814 chr19:38878550-38878559 chr19:38878009-38878018 chr19:38878008-38878020 chr19:38879102-38879111 chr19:38878722-38878733 chr19:38879468-38879477 chr19:38878549-38878559 chr19:38878706-38878715 chr19:38878549-38878558 chr19:38878570-38878584 chr19:38878916-38878925 chr19:38878570-38878580 chr19:38879467-38879479 chr19:38878248-38878262 chr19:38878705-38878714 chr19:38878750-38878759 chr19:38878805-38878814 chr19:38878008-38878020 chr19:38878804-38878813 chr19:38878009-38878019 chr19:38879468-38879478 chr19:38878751-38878760 chr19:38879019-38879028 chr19:38878548-38878560
49	RCOR1	chr19:38877836-38878525	K562	blood:	n/a	n/a
50	MYC	chr19:38877726-38878800	K562	blood:	n/a	chr19:38878570-38878580 chr19:38878754-38878763 chr19:38878750-38878760

No.	Distal block	Cell Line	Cell type
1	chr19:38876175..38878484-chr19:38901904..38903905,2	K562	blood:
2	chr19:38851103..38853998-chr19:38877778..38880419,3	K562	blood:
3	chr19:38873942..38878444-chr19:38892255..38895006,5	K562	blood:
4	chr19:38805296..38807779-chr19:38877097..38880049,2	K562	blood:
5	chr19:36630602..36632414-chr19:38875371..38878496,3	MCF-7	breast:
6	chr19:38851827..38854715-chr19:38877414..38880419,4	K562	blood:
7	chr19:38717810..38720228-chr19:38876711..38878921,2	K562	blood:
8	chr19:38724122..38725097-chr19:38877454..38878445,2	K562	blood:
9	chr19:38851829..38853788-chr19:38876902..38878905,2	MCF-7	breast:
10	chr19:38824957..38829265-chr19:38874295..38879043,8	MCF-7	breast:
11	chr19:38825387..38828116-chr19:38877119..38879831,3	MCF-7	breast:

Variant related genes	Relation type
SPRED3	TF binding region
ENSG00000130244	Chromatin interaction
ENSG00000171777	Chromatin interaction
ENSG00000266963	Chromatin interaction
ENSG00000126247	Chromatin interaction
ENSG00000167645	Chromatin interaction
ENSG00000011332	Chromatin interaction
ENSG00000099338	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10993	1.00[CEU][hapmap]
rs11083454	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11538289	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11880301	1.00[CEU][hapmap]
rs2074981	0.81[TSI][hapmap]
rs2302228	1.00[EUR][1000 genomes]
rs3745955	0.80[EUR][1000 genomes]
rs3745963	1.00[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3760884	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3786874	0.81[TSI][hapmap]
rs57753437	0.93[EUR][1000 genomes]
rs59491640	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60780508	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508791	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6508792	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6508793	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7245668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246191	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7246213	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7248540	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7257976	1.00[CEU][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73043029	0.81[EUR][1000 genomes]
rs73043030	0.93[EUR][1000 genomes]
rs73043033	0.93[EUR][1000 genomes]
rs73043098	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73044905	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044908	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044911	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044917	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044919	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044923	0.80[EUR][1000 genomes]
rs73044926	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044928	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044930	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044932	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044937	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044942	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044944	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044946	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044947	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044948	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73044953	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8108440	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8109713	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8112499	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063471	chr19:38734744-39148392	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	73 gene(s)	inside rSNPs	diseases
2	nsv833822	chr19:38760748-38945105	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv911658	chr19:38785318-39002140	Genic enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv470140	chr19:38840139-39119494	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
5	nsv911659	chr19:38852357-39002140	Active TSS Bivalent/Poised TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
6	nsv911660	chr19:38852357-39060238	Flanking Active TSS Bivalent Enhancer Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv833823	chr19:38855550-39035800	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv1064275	chr19:38859865-38913251	Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
9	nsv911661	chr19:38872335-38894829	Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
10	nsv911662	chr19:38872634-38895809	Flanking Active TSS Enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
11	esv1803709	chr19:38874828-38900078	Enhancers Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38874800-38878200	Weak transcription	HSMMtube	muscle
2	chr19:38875200-38878400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr19:38875200-38878400	Weak transcription	Aorta	Aorta
4	chr19:38875800-38878200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
5	chr19:38876200-38880200	Enhancers	Fetal Heart	heart
6	chr19:38876400-38880600	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr19:38876600-38878200	Bivalent Enhancer	Fetal Stomach	stomach
8	chr19:38876600-38878600	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr19:38876600-38879200	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
10	chr19:38876800-38878200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr19:38876800-38878400	Bivalent Enhancer	Fetal Thymus	thymus
12	chr19:38876800-38879000	Flanking Active TSS	Primary hematopoietic stem cells	blood
13	chr19:38876800-38879200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr19:38876800-38880200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr19:38876800-38881400	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr19:38877000-38878200	Enhancers	Right Ventricle	heart
17	chr19:38877000-38878200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr19:38877000-38879400	Enhancers	Lung	lung
19	chr19:38877200-38878200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr19:38877200-38878200	Enhancers	Left Ventricle	heart
21	chr19:38877200-38878200	Enhancers	NH-A	brain
22	chr19:38877200-38879200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
23	chr19:38877200-38880200	Flanking Active TSS	Dnd41	blood
24	chr19:38877400-38878200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:38877400-38878200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr19:38877400-38878200	Enhancers	Psoas Muscle	Psoas
27	chr19:38877400-38878200	Enhancers	Small Intestine	intestine
28	chr19:38877400-38878200	Enhancers	Spleen	Spleen
29	chr19:38877400-38878400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr19:38877400-38879000	Bivalent Enhancer	Fetal Lung	lung
31	chr19:38877400-38881000	Active TSS	HUES48 Cell Line	embryonic stem cell
32	chr19:38877400-38881200	Active TSS	iPS-20b Cell Line	embryonic stem cell
33	chr19:38877600-38878200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
34	chr19:38877600-38878200	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
35	chr19:38877600-38878200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr19:38877600-38878200	Enhancers	Liver	Liver
37	chr19:38877600-38878200	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr19:38877600-38878200	Flanking Active TSS	Esophagus	oesophagus
39	chr19:38877600-38878200	Flanking Active TSS	NHEK	skin
40	chr19:38877600-38878400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr19:38877600-38878400	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
42	chr19:38877600-38878400	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
43	chr19:38877600-38878400	Flanking Active TSS	K562	blood
44	chr19:38877600-38878600	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr19:38877600-38878600	Flanking Active TSS	Colonic Mucosa	Colon
46	chr19:38877600-38878800	Flanking Active TSS	Primary B cells from cord blood	blood
47	chr19:38877600-38879000	Flanking Active TSS	Primary T cells from cord blood	blood
48	chr19:38877600-38879200	Flanking Bivalent TSS/Enh	Primary monocytes fromperipheralblood	blood
49	chr19:38877600-38879200	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
50	chr19:38877600-38879200	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood

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