Variant report

Variant	rs7249890
Chromosome Location	chr19:40441024-40441025
allele	C/T
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	BCL3	chr19:40440742-40441792	A549	lung:	n/a	n/a
2	MAX	chr19:40440679-40441225	A549	lung:	n/a	chr19:40440960-40440967 chr19:40440958-40440969 chr19:40440959-40440968 chr19:40440961-40440977 chr19:40440958-40440968 chr19:40440958-40440969 chr19:40440959-40440968
3	CTCF	chr19:40441020-40441170	GM12870	blood:	n/a	n/a
4	MAX	chr19:40440563-40441302	A549	lung:	n/a	chr19:40440960-40440967 chr19:40440958-40440969 chr19:40440959-40440968 chr19:40440961-40440977 chr19:40440958-40440968 chr19:40440958-40440969 chr19:40440959-40440968
5	TCF12	chr19:40440113-40444572	A549	lung:	n/a	chr19:40442444-40442454 chr19:40442130-40442140 chr19:40442317-40442326 chr19:40440845-40440855 chr19:40441092-40441102
6	MAX	chr19:40440916-40441093	A549	lung:	n/a	chr19:40440960-40440967 chr19:40440958-40440969 chr19:40440959-40440968 chr19:40440961-40440977 chr19:40440958-40440968 chr19:40440958-40440969 chr19:40440959-40440968

Variant related genes	Relation type
FCGBP	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs170900	0.82[GIH][hapmap]
rs2231738	0.93[ASW][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.86[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.89[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs234365	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2355720	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3760919	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs3760923	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3786938	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826919	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs424365	0.81[ASN][1000 genomes]
rs7249286	0.82[GIH][hapmap]
rs8106269	0.93[ASW][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs8109718	0.84[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs8109879	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9749001	0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
2	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv510766	chr19:40344356-40453018	Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv917321	chr19:40403192-40694875	Strong transcription Flanking Active TSS Weak transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:40 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40420200-40441800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr19:40438600-40443800	Enhancers	Primary T cells fromperipheralblood	blood
3	chr19:40439800-40443800	Enhancers	Primary T helper cells fromperipheralblood	blood
4	chr19:40439800-40443800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr19:40439800-40443800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
6	chr19:40439800-40444600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
7	chr19:40440000-40443800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
8	chr19:40440000-40443800	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr19:40440000-40444000	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr19:40440000-40444000	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr19:40440000-40444200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr19:40440000-40444200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr19:40440200-40443800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr19:40440400-40441400	Enhancers	A549	lung
15	chr19:40440400-40443600	Enhancers	Spleen	Spleen
16	chr19:40440400-40443800	Enhancers	Primary B cells from peripheral blood	blood
17	chr19:40440600-40441200	Enhancers	Gastric	stomach
18	chr19:40440600-40441800	Enhancers	Esophagus	oesophagus
19	chr19:40440600-40442600	Bivalent Enhancer	Placenta	Placenta
20	chr19:40440600-40442800	Enhancers	Sigmoid Colon	Sigmoid Colon
21	chr19:40440600-40443800	Enhancers	Primary T cells from cord blood	blood
22	chr19:40440600-40443800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
23	chr19:40440600-40444000	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
24	chr19:40440800-40441400	Enhancers	Stomach Mucosa	stomach
25	chr19:40440800-40441600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr19:40440800-40443000	Enhancers	Primary B cells from cord blood	blood
27	chr19:40440800-40443600	Enhancers	Colonic Mucosa	Colon
28	chr19:40440800-40443800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
29	chr19:40440800-40444000	Enhancers	Fetal Intestine Small	intestine
30	chr19:40440800-40444600	Enhancers	Fetal Intestine Large	intestine
31	chr19:40440800-40447000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr19:40441000-40441200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr19:40441000-40441400	Enhancers	Brain Hippocampus Middle	brain
34	chr19:40441000-40441400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
35	chr19:40441000-40441600	Weak transcription	Lung	lung
36	chr19:40441000-40441800	Enhancers	Rectal Mucosa Donor 29	rectum
37	chr19:40441000-40443000	Enhancers	Duodenum Mucosa	Duodenum
38	chr19:40441000-40443200	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
39	chr19:40441000-40443800	Enhancers	Rectal Mucosa Donor 31	rectum
40	chr19:40441000-40443800	Enhancers	GM12878-XiMat	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links