Variant report

Variant	rs10423648
Chromosome Location	chr19:35838743-35838744
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	USF2	chr19:35837485-35839010	GM12878	blood:	n/a	n/a
2	NFIC	chr19:35837299-35838965	GM12878	blood:	n/a	n/a
3	CUX1	chr19:35837331-35839042	GM12878	blood:	n/a	n/a
4	BHLHE40	chr19:35836713-35839191	GM12878	blood:	n/a	n/a
5	YY1	chr19:35838081-35838906	GM12878	blood:	n/a	n/a
6	EP300	chr19:35838281-35839120	GM12878	blood:	n/a	n/a
7	ATF2	chr19:35837247-35839038	GM12878	blood:	n/a	n/a
8	FOXM1	chr19:35837220-35839303	GM12878	blood:	n/a	n/a
9	POLR2A	chr19:35834081-35844229	GM12878	blood:	n/a	n/a
10	PAX5	chr19:35838145-35838986	GM12878	blood:	n/a	n/a
11	CEBPB	chr19:35838654-35838804	IMR90	lung:	n/a	chr19:35838744-35838755 chr19:35838744-35838757
12	POU2F2	chr19:35837429-35838951	GM12878	blood:	n/a	chr19:35838670-35838677 chr19:35838668-35838678 chr19:35838666-35838681 chr19:35838665-35838683 chr19:35838667-35838681 chr19:35838667-35838679 chr19:35838668-35838678 chr19:35838669-35838678
13	POLR2A	chr19:35836311-35839226	GM12878	blood:	n/a	n/a
14	CHD1	chr19:35837266-35839139	GM12878	blood:	n/a	n/a
15	ATF2	chr19:35837301-35839275	GM12878	blood:	n/a	n/a
16	YY1	chr19:35838068-35838887	GM12892	blood:	n/a	n/a
17	BCL3	chr19:35837388-35839100	GM12878	blood:	n/a	n/a
18	POLR2A	chr19:35836562-35839254	GM18951	blood:	n/a	n/a
19	CEBPB	chr19:35838565-35838934	K562	blood:	n/a	chr19:35838744-35838755 chr19:35838744-35838757
20	POLR2A	chr19:35836286-35839245	GM12892	blood:	n/a	n/a
21	POLR2A	chr19:35836339-35843943	GM19193	blood:	n/a	n/a
22	EP300	chr19:35836855-35839120	GM12878	blood:	n/a	n/a
23	EP300	chr19:35837269-35838959	GM12878	blood:	n/a	n/a
24	PML	chr19:35836159-35841607	GM12878	blood:	n/a	n/a
25	SMC3	chr19:35838288-35839113	GM12878	blood:	n/a	n/a
26	SP1	chr19:35838168-35838854	GM12878	blood:	n/a	n/a
27	CREB1	chr19:35837266-35839064	GM12878	blood:	n/a	n/a
28	MTA3	chr19:35837234-35839313	GM12878	blood:	n/a	n/a
29	BCLAF1	chr19:35836768-35839223	GM12878	blood:	n/a	chr19:35839148-35839157
30	PAX5	chr19:35838112-35839042	GM12878	blood:	n/a	n/a
31	TBP	chr19:35838300-35838916	GM12878	blood:	n/a	n/a
32	RELA	chr19:35836740-35839176	GM18951	blood:	n/a	n/a
33	POU2F2	chr19:35838359-35838967	GM12891	blood:	n/a	chr19:35838670-35838677 chr19:35838668-35838678 chr19:35838666-35838681 chr19:35838665-35838683 chr19:35838667-35838681 chr19:35838667-35838679 chr19:35838668-35838678 chr19:35838669-35838678
34	RELA	chr19:35836498-35839120	GM18505	blood:	n/a	n/a
35	POLR2A	chr19:35836392-35841540	GM12878	blood:	n/a	n/a
36	TCF12	chr19:35838336-35838845	GM12878	blood:	n/a	n/a
37	NFATC1	chr19:35838085-35839343	GM12878	blood:	n/a	n/a
38	FAM48A	chr19:35838671-35838759	GM12878	blood:	n/a	n/a
39	RELA	chr19:35837316-35839118	GM19099	blood:	n/a	n/a
40	SPI1	chr19:35838424-35838984	HL-60	blood:	n/a	chr19:35838692-35838705
41	TCF3	chr19:35838353-35838777	GM12878	blood:	n/a	n/a
42	PML	chr19:35838060-35838838	GM12878	blood:	n/a	n/a
43	YY1	chr19:35838030-35838849	GM12891	blood:	n/a	n/a
44	ELF1	chr19:35838143-35838895	GM12878	blood:	n/a	n/a
45	POU2F2	chr19:35837416-35839185	GM12891	blood:	n/a	chr19:35838670-35838677 chr19:35838668-35838678 chr19:35838666-35838681 chr19:35838665-35838683 chr19:35838667-35838681 chr19:35838667-35838679 chr19:35838668-35838678 chr19:35838669-35838678
46	SPI1	chr19:35838173-35839152	GM12878	blood:	n/a	chr19:35838692-35838705 chr19:35839044-35839051
47	YY1	chr19:35837352-35838961	GM12878	blood:	n/a	n/a
48	SP1	chr19:35838196-35838845	GM12878	blood:	n/a	n/a
49	PAX5	chr19:35838198-35838948	GM12878	blood:	n/a	n/a
50	POLR2A	chr19:35838016-35839051	GM12891	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr19:35838211..35841126-chr19:35842051..35843758,2	K562	blood:
2	chr19:35838470..35841134-chr19:35848339..35849864,2	MCF-7	breast:
3	chr19:35759183..35761582-chr19:35836760..35840257,3	MCF-7	breast:
4	chr19:35837012..35839854-chr19:35847612..35849842,2	MCF-7	breast:

Variant related genes	Relation type
FFAR1	TF binding region
ENSG00000185897	Chromatin interaction
ENSG00000105698	Chromatin interaction
ENSG00000126266	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10406829	1.00[MEX][hapmap]
rs10426830	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16970196	1.00[MEX][hapmap]
rs16970204	1.00[MEX][hapmap]
rs16970264	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3088063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58174206	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7247137	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8108571	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][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	nsv432045	chr19:35556260-36520760	Flanking Active TSS Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1060100	chr19:35658505-36170042	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
3	nsv543993	chr19:35658505-36170042	Enhancers Strong transcription Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
4	nsv510765	chr19:35708226-35890668	Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
5	esv2758497	chr19:35711078-35887113	Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
6	esv2758758	chr19:35711078-35887113	Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
7	nsv833810	chr19:35782588-35971959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases
8	esv1828194	chr19:35812566-35865695	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
9	nsv1067129	chr19:35827036-35849310	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
10	nsv173	chr19:35837405-35866835	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv2471	chr19:35837405-35903115	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10423648	FFAR1	cis	multi-tissue	Pritchard
rs10423648	FFAR1	cis	lymphoblastoid	seeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35817600-35844000	Weak transcription	Brain Angular Gyrus	brain
2	chr19:35832800-35838800	Strong transcription	Brain Inferior Temporal Lobe	brain
3	chr19:35835600-35839800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr19:35835800-35840000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:35836400-35840400	Enhancers	Primary hematopoietic stem cells	blood
6	chr19:35836600-35839000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
7	chr19:35836600-35839000	Bivalent Enhancer	Placenta	Placenta
8	chr19:35836600-35839200	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
9	chr19:35836600-35839800	Enhancers	Fetal Thymus	thymus
10	chr19:35836800-35838800	Enhancers	HepG2	liver
11	chr19:35836800-35839200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:35836800-35839200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr19:35836800-35843800	Weak transcription	Brain Cingulate Gyrus	brain
14	chr19:35836800-35848000	Weak transcription	Brain Substantia Nigra	brain
15	chr19:35837000-35839200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr19:35837000-35839200	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
17	chr19:35837000-35839200	Enhancers	Duodenum Mucosa	Duodenum
18	chr19:35837400-35839200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
19	chr19:35837400-35839200	Bivalent Enhancer	Dnd41	blood
20	chr19:35837400-35839400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr19:35837400-35840800	Enhancers	Spleen	Spleen
22	chr19:35837600-35843600	Weak transcription	Brain Anterior Caudate	brain
23	chr19:35837800-35838800	Enhancers	Thymus	Thymus
24	chr19:35837800-35839000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr19:35838000-35838800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr19:35838000-35839000	Flanking Active TSS	Primary B cells from cord blood	blood
27	chr19:35838200-35838800	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr19:35838200-35839000	Flanking Active TSS	GM12878-XiMat	blood
29	chr19:35838200-35840000	Weak transcription	Ovary	ovary
30	chr19:35838200-35840800	Enhancers	Primary hematopoietic stem cells short term culture	blood
31	chr19:35838200-35849200	Weak transcription	Brain Hippocampus Middle	brain
32	chr19:35838400-35839200	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr19:35838400-35839200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
34	chr19:35838400-35839200	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr19:35838400-35842200	Enhancers	Primary B cells from peripheral blood	blood
36	chr19:35838600-35839000	Enhancers	Primary T cells from cord blood	blood
37	chr19:35838600-35839000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr19:35838600-35839200	Enhancers	Primary T helper naive cells from peripheral blood	blood
39	chr19:35838600-35839200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
40	chr19:35838600-35839800	Enhancers	Monocytes-CD14+_RO01746	blood
41	chr19:35838600-35840000	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr19:35838600-35843600	Weak transcription	K562	blood

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