Variant report

Variant	rs241951
Chromosome Location	chr19:38270163-38270164
allele	A/C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:367)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:367 , 50 per page) page: 1 2 3 4 5 6 7 8

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CREB1	chr19:38269528-38270531	GM12878	blood:	n/a	n/a
2	EP300	chr19:38270127-38270548	HepG2	liver:	n/a	n/a
3	POLR2A	chr19:38269619-38270633	Hela-S3	cervix:	n/a	n/a
4	YY1	chr19:38269851-38270521	HCT-116	colon:	n/a	n/a
5	ATF1	chr19:38269848-38270362	K562	blood:	n/a	n/a
6	ZMIZ1	chr19:38270071-38270367	K562	blood:	n/a	n/a
7	POLR2A	chr19:38270010-38270614	A549	lung:	n/a	n/a
8	TAF1	chr19:38269946-38270514	PFSK-1	brain:	n/a	n/a
9	ELK1	chr19:38270156-38270452	K562	blood:	n/a	n/a
10	MAX	chr19:38269951-38270641	A549	lung:	n/a	n/a
11	GABPA	chr19:38270008-38270414	K562	blood:	n/a	n/a
12	SIN3AK20	chr19:38269443-38270769	MCF-7	breast:	n/a	n/a
13	E2F6	chr19:38269664-38270877	A549	lung:	n/a	n/a
14	SIX5	chr19:38270050-38270439	K562	blood:	n/a	n/a
15	MAX	chr19:38269755-38270637	H1-hESC	embryonic stem cell:	n/a	n/a
16	POLR2A	chr19:38269704-38270676	GM12878	blood:	n/a	n/a
17	TAF1	chr19:38269699-38270660	ECC-1	luminal epithelium:	n/a	n/a
18	ELF1	chr19:38270041-38270422	HepG2	liver:	n/a	n/a
19	ZNF143	chr19:38269904-38270598	H1-hESC	embryonic stem cell:	n/a	n/a
20	POLR2A	chr19:38269754-38270689	K562	blood:	n/a	n/a
21	ELF1	chr19:38269880-38270347	K562	blood:	n/a	n/a
22	POLR2A	chr19:38269939-38270631	HCT-116	colon:	n/a	n/a
23	TAF1	chr19:38270099-38270660	Hela-S3	cervix:	n/a	n/a
24	MYC	chr19:38270136-38270259	MCF-7	breast:	n/a	n/a
25	RCOR1	chr19:38269684-38270392	GM12878	blood:	n/a	n/a
26	MAX	chr19:38269715-38270685	GM12878	blood:	n/a	n/a
27	TCF12	chr19:38270111-38270659	GM12878	blood:	n/a	n/a
28	REST	chr19:38269429-38270828	H1-neurons	neurons:	n/a	chr19:38270079-38270089 chr19:38269734-38269744
29	TAF1	chr19:38269889-38270652	H1-hESC	embryonic stem cell:	n/a	n/a
30	POLR2A	chr19:38270030-38270567	HepG2	liver:	n/a	n/a
31	TBP	chr19:38269728-38270512	GM12878	blood:	n/a	n/a
32	STAT5A	chr19:38269857-38270513	GM12878	blood:	n/a	n/a
33	BHLHE40	chr19:38269709-38270586	K562	blood:	n/a	chr19:38269965-38269978
34	MYC	chr19:38269959-38270301	K562	blood:	n/a	n/a
35	REST	chr19:38269947-38270601	HepG2	liver:	n/a	chr19:38270079-38270089
36	YY1	chr19:38270043-38270398	K562	blood:	n/a	n/a
37	POLR2A	chr19:38269933-38270625	HCT-116	colon:	n/a	n/a
38	POLR2A	chr19:38269182-38270883	HepG2	liver:	n/a	n/a
39	TCF12	chr19:38269904-38270589	ECC-1	luminal epithelium:	n/a	n/a
40	PAX5	chr19:38269633-38270399	GM12878	blood:	n/a	n/a
41	ETS1	chr19:38269580-38270796	A549	lung:	n/a	chr19:38270640-38270647 chr19:38270067-38270080
42	POLR2A	chr19:38269956-38270632	HepG2	liver:	n/a	n/a
43	MAX	chr19:38269486-38270754	NB4	blood:	n/a	n/a
44	ELK4	chr19:38269805-38270600	Hela-S3	cervix:	n/a	n/a
45	POLR2A	chr19:38269641-38270775	HL-60	blood:	n/a	n/a
46	HCFC1	chr19:38269236-38271180	Hela-S3	cervix:	n/a	n/a
47	SP1	chr19:38269683-38270760	A549	lung:	n/a	chr19:38270611-38270620 chr19:38270610-38270622
48	YY1	chr19:38270104-38270350	HCT-116	colon:	n/a	n/a
49	POLR2A	chr19:38269673-38270698	GM12891	blood:	n/a	n/a
50	POLR2A	chr19:38269696-38270678	GM19193	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr19:38085182..38087082-chr19:38268049..38270346,2	K562	blood:
2	chr19:38261551..38263090-chr19:38267286..38270188,2	K562	blood:
3	chr19:38269810..38270643-chrX:77154544..77155428,2	Hela-S3	cervix:
4	chr19:38270038..38270580-chr19:38864807..38865462,2	Hela-S3	cervix:
5	chr19:37956743..37958791-chr19:38268721..38270290,2	K562	blood:
6	chr19:38084603..38087452-chr19:38269351..38271925,3	MCF-7	breast:
7	chr19:38269888..38270734-chr22:43010932..43011476,2	HCT-116	colon:
8	chr19:38259097..38263090-chr19:38267286..38270188,4	K562	blood:
9	chr19:37995858..37997705-chr19:38268751..38270937,2	MCF-7	breast:
10	chr19:38261286..38264562-chr19:38269904..38271542,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000267422	TF binding region
ENSG00000171827	Chromatin interaction
ENSG00000171817	Chromatin interaction
ENSG00000131174	Chromatin interaction
ENSG00000100227	Chromatin interaction
ENSG00000189144	Chromatin interaction
ENSG00000270022	Chromatin interaction
ENSG00000099341	Chromatin interaction
ENSG00000266916	Chromatin interaction
ENSG00000180479	Chromatin interaction
ENSG00000196437	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10406856	0.89[EUR][1000 genomes]
rs10418133	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10421572	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10422056	0.90[CHB][hapmap]
rs10425671	0.90[CHB][hapmap]
rs10426553	0.88[EUR][1000 genomes]
rs10426712	0.88[EUR][1000 genomes]
rs11083439	0.90[CHB][hapmap]
rs11668434	0.90[CHB][hapmap]
rs11668558	0.90[CHB][hapmap]
rs11672077	1.00[CHB][hapmap]
rs1643470	0.90[CHB][hapmap]
rs17306508	0.90[CHB][hapmap]
rs17306795	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1871197	1.00[CHB][hapmap]
rs2160640	0.90[CHB][hapmap]
rs2382622	0.86[EUR][1000 genomes]
rs241937	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs241940	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs241941	0.90[CHB][hapmap]
rs241942	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs241948	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs2927743	0.84[CEU][hapmap]
rs2972456	1.00[CHB][hapmap]
rs2972459	1.00[CHB][hapmap]
rs35462777	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3752365	0.90[CHB][hapmap]
rs3894129	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs4482404	0.90[CHB][hapmap]
rs4802132	0.89[EUR][1000 genomes]
rs4802133	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs4802134	0.90[CHB][hapmap]
rs4802137	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55970469	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs56851463	0.89[EUR][1000 genomes]
rs57268445	0.89[EUR][1000 genomes]
rs6508738	1.00[CHB][hapmap]
rs6508747	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6508750	1.00[CEU][hapmap]
rs697433	0.89[CHB][hapmap]
rs7245957	0.86[EUR][1000 genomes]
rs7254170	1.00[CHB][hapmap]
rs7254828	0.90[CHB][hapmap];0.84[CHD][hapmap]
rs8100684	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs8101131	0.89[EUR][1000 genomes]
rs8111400	0.90[CHB][hapmap]
rs856302	0.90[CHB][hapmap];0.92[CHD][hapmap]
rs953370	0.84[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];1.00[LWK][hapmap];0.92[MKK][hapmap];0.91[TSI][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv579468	chr19:37977609-38293487	ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv833820	chr19:38190721-38414049	Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs241951	PAFAH1B3	cis	cerebellum	SCAN
rs241951	PLEKHG2	cis	cerebellum	SCAN
rs241951	AKT2	cis	parietal	SCAN
rs241951	IRGQ	cis	parietal	SCAN
rs241951	AC012309.5	cis	Thyroid	GTEx
rs241951	PHLDB3	cis	cerebellum	SCAN
rs241951	PPP5C	cis	parietal	SCAN
rs241951	CEACAM19	cis	cerebellum	SCAN
rs241951	ZNF226	cis	cerebellum	SCAN
rs241951	DMPK	cis	parietal	SCAN
rs241951	AC012309.5	cis	Artery Tibial	GTEx
rs241951	AC012309.5	cis	Heart Left Ventricle	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38269000-38270800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38269200-38270200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
3	chr19:38269200-38270600	Active TSS	Pancreatic Islets	Pancreatic Islet
4	chr19:38269200-38270800	Active TSS	Brain Cingulate Gyrus	brain
5	chr19:38269200-38270800	Active TSS	Fetal Intestine Small	intestine
6	chr19:38269200-38270800	Active TSS	HSMM	muscle
7	chr19:38269200-38271000	Active TSS	HUES64 Cell Line	embryonic stem cell
8	chr19:38269200-38271000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr19:38269200-38271000	Active TSS	Brain Hippocampus Middle	brain
10	chr19:38269200-38271000	Active TSS	A549	lung
11	chr19:38269200-38271200	Active TSS	H1 Cell Line	embryonic stem cell
12	chr19:38269200-38271200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr19:38269200-38271200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr19:38269200-38271200	Active TSS	HUES48 Cell Line	embryonic stem cell
15	chr19:38269200-38271200	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr19:38269200-38271200	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr19:38269200-38271200	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr19:38269200-38271200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:38269200-38271200	Active TSS	GM12878-XiMat	blood
20	chr19:38269200-38271200	Active TSS	HMEC	breast
21	chr19:38269200-38271400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr19:38269400-38270800	Active TSS	H9 Cell Line	embryonic stem cell
23	chr19:38269400-38270800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr19:38269400-38270800	Active TSS	Placenta Amnion	Placenta Amnion
25	chr19:38269400-38271000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
26	chr19:38269400-38271000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr19:38269400-38271000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr19:38269400-38271000	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:38269400-38271200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr19:38269400-38271200	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr19:38269400-38271200	Active TSS	NHLF	lung
32	chr19:38269600-38270200	Active TSS	Primary T helper naive cells fromperipheralblood	blood
33	chr19:38269600-38270400	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr19:38269600-38270400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
35	chr19:38269600-38270400	Active TSS	Primary T regulatory cells fromperipheralblood	blood
36	chr19:38269600-38270600	Active TSS	Primary T cells from cord blood	blood
37	chr19:38269600-38270600	ZNF genes & repeats	Fetal Brain Male	brain
38	chr19:38269600-38270600	Active TSS	Gastric	stomach
39	chr19:38269600-38270800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
40	chr19:38269600-38270800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:38269600-38270800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
42	chr19:38269600-38270800	Active TSS	Breast Myoepithelial Primary Cells	Breast
43	chr19:38269600-38270800	Active TSS	Primary T helper naive cells from peripheral blood	blood
44	chr19:38269600-38270800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr19:38269600-38270800	Active TSS	Aorta	Aorta
46	chr19:38269600-38270800	Active TSS	Duodenum Smooth Muscle	Duodenum
47	chr19:38269600-38270800	Active TSS	Esophagus	oesophagus
48	chr19:38269600-38270800	Active TSS	Fetal Intestine Large	intestine
49	chr19:38269600-38270800	Active TSS	Fetal Thymus	thymus
50	chr19:38269600-38270800	Active TSS	Left Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links