Variant report

Variant	rs3746248
Chromosome Location	chr19:35790503-35790504
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:35785237..35787422-chr19:35789802..35791961,2	MCF-7	breast:
2	chr19:35742830..35745421-chr19:35788824..35790578,2	MCF-7	breast:
3	chr19:35788326..35791177-chr19:35803354..35807024,3	MCF-7	breast:
4	chr19:35788362..35791092-chr19:35794304..35796037,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000271366	Chromatin interaction

Extended variants
information (count: 21 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10418687	0.93[EUR][1000 genomes]
rs11879566	0.83[EUR][1000 genomes]
rs12185485	0.87[CEU][hapmap];0.88[TSI][hapmap];0.82[EUR][1000 genomes]
rs12974994	0.93[EUR][1000 genomes]
rs28505365	0.80[EUR][1000 genomes]
rs73031739	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv911618	chr19:35734107-35807845	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
8	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
9	esv3399211	chr19:35786312-35791010	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
10	esv3329030	chr19:35786312-35791110	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
11	esv3379757	chr19:35786412-35791110	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
12	esv3447618	chr19:35786412-35791110	Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
13	esv3452034	chr19:35786812-35790910	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
14	esv3391577	chr19:35789737-35792285	Genic enhancers Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a
15	esv3380994	chr19:35789962-35792160	Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3746248	PSG4	cis	parietal	SCAN
rs3746248	SERTAD1	cis	parietal	SCAN
rs3746248	SHKBP1	cis	cerebellum	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:35774800-35809600	Weak transcription	Right Atrium	heart
2	chr19:35787200-35790600	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr19:35788200-35791800	Genic enhancers	Brain Substantia Nigra	brain
4	chr19:35788800-35791400	Genic enhancers	Brain Inferior Temporal Lobe	brain
5	chr19:35788800-35795000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr19:35789200-35793400	Weak transcription	Spleen	Spleen
7	chr19:35789200-35796800	Genic enhancers	Brain Cingulate Gyrus	brain
8	chr19:35789400-35794600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:35789600-35796200	Weak transcription	Primary B cells from peripheral blood	blood
10	chr19:35789600-35796600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr19:35789800-35791200	Weak transcription	Gastric	stomach
12	chr19:35790000-35791000	Weak transcription	Pancreas	Pancrea
13	chr19:35790000-35791200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr19:35790000-35797800	Weak transcription	Fetal Kidney	kidney
15	chr19:35790200-35791000	Enhancers	Brain Hippocampus Middle	brain
16	chr19:35790200-35791200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr19:35790200-35792200	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr19:35790200-35794000	Weak transcription	Brain Anterior Caudate	brain
19	chr19:35790200-35794200	Weak transcription	Brain Angular Gyrus	brain
20	chr19:35790200-35796400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr19:35790400-35790600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr19:35790400-35790600	Flanking Active TSS	K562	blood
23	chr19:35790400-35791600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
24	chr19:35790400-35792200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell

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