Variant report

Variant	rs3826706
Chromosome Location	chr19:42793590-42793591
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	POLR2A	chr19:42793490-42793726	HepG2	liver:	n/a	n/a
2	ZNF263	chr19:42793348-42793736	HEK293-T-REx	kidney:	n/a	chr19:42793529-42793550
3	POLR2A	chr19:42792419-42793763	SK-N-MC	brain:	n/a	n/a
4	JUND	chr19:42793369-42793721	HepG2	liver:	n/a	n/a
5	POLR2A	chr19:42793092-42793725	PFSK-1	brain:	n/a	n/a
6	CEBPB	chr19:42793512-42793646	A549	lung:	n/a	n/a
7	JUN	chr19:42793450-42793646	HepG2	liver:	n/a	chr19:42793543-42793556

No.	Distal block	Cell Line	Cell type
1	chr19:42744297..42761073-chr19:42776978..42802286,113	MCF-7	breast:
2	chr19:42792212..42794667-chr19:42800851..42802759,2	MCF-7	breast:
3	chr19:42786948..42794333-chr19:42803465..42809501,23	K562	blood:
4	chr19:42704086..42706332-chr19:42793482..42795318,2	K562	blood:
5	chr19:42743599..42762610-chr19:42780302..42801550,102	MCF-7	breast:
6	chr19:42792606..42794185-chr5:2751901..2753503,2	MCF-7	breast:

Variant related genes	Relation type
CIC	TF binding region
ENSG00000268643	Chromatin interaction
ENSG00000204957	Chromatin interaction
ENSG00000170561	Chromatin interaction
ENSG00000186493	Chromatin interaction
ENSG00000105722	Chromatin interaction
ENSG00000105723	Chromatin interaction
ENSG00000079462	Chromatin interaction
ENSG00000188368	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10500285	1.00[YRI][hapmap]
rs1206032	0.88[CEU][hapmap];0.95[GIH][hapmap];0.81[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap]
rs16975684	1.00[YRI][hapmap]
rs17342284	1.00[YRI][hapmap]
rs2267630	1.00[YRI][hapmap]
rs3810151	1.00[YRI][hapmap]
rs4803531	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7248379	1.00[YRI][hapmap]

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	nsv522854	chr19:42120283-42931004	Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv520239	chr19:42357455-42931004	Flanking Active TSS Enhancers Bivalent Enhancer Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	esv1805469	chr19:42367635-42798851	Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
4	nsv911782	chr19:42514712-42931004	Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
5	nsv1055554	chr19:42619671-42821642	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
6	nsv526186	chr19:42676481-43203507	Enhancers Bivalent Enhancer Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases
7	esv2422471	chr19:42733141-43669485	Genic enhancers Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
8	nsv833834	chr19:42736444-42835027	Genic enhancers Flanking Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	42 gene(s)	inside rSNPs	diseases
9	nsv911785	chr19:42741124-42917545	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
10	nsv911786	chr19:42744234-42797959	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	39 gene(s)	inside rSNPs	diseases
11	nsv911787	chr19:42773862-42795554	Active TSS Genic enhancers Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3826706	SULT1A1	trans	parietal	SCAN
rs3826706	CCDC8	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:42790200-42795400	Weak transcription	Hela-S3	cervix
2	chr19:42790200-42800200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr19:42790400-42794800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr19:42790600-42793800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr19:42790600-42794000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr19:42790600-42797800	Genic enhancers	Fetal Muscle Trunk	muscle
7	chr19:42790600-42801600	Strong transcription	Dnd41	blood
8	chr19:42790600-42802400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr19:42790600-42804600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr19:42790600-42804800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:42790600-42805000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr19:42790600-42805400	Weak transcription	Stomach Mucosa	stomach
13	chr19:42790600-42806000	Weak transcription	Psoas Muscle	Psoas
14	chr19:42790800-42794200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr19:42790800-42794400	Strong transcription	A549	lung
16	chr19:42790800-42794600	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr19:42790800-42799000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr19:42790800-42802000	Strong transcription	Cortex derived primary cultured neurospheres	brain
19	chr19:42790800-42802200	Strong transcription	Thymus	Thymus
20	chr19:42791000-42794000	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr19:42791000-42794000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr19:42791000-42795000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:42791000-42795000	Strong transcription	Fetal Thymus	thymus
24	chr19:42791000-42795200	Strong transcription	NHEK	skin
25	chr19:42791000-42795800	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr19:42791000-42796000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr19:42791000-42799200	Strong transcription	HUES64 Cell Line	embryonic stem cell
28	chr19:42791000-42799600	Strong transcription	HSMMtube	muscle
29	chr19:42791000-42799800	Strong transcription	Lung	lung
30	chr19:42791000-42800200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
31	chr19:42791000-42800200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr19:42791000-42801400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr19:42791000-42801600	Strong transcription	Muscle Satellite Cultured Cells	--
34	chr19:42791000-42801600	Strong transcription	NHLF	lung
35	chr19:42791000-42802800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr19:42791200-42793600	Weak transcription	Fetal Kidney	kidney
37	chr19:42791200-42793800	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
38	chr19:42791200-42794400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
39	chr19:42791200-42794400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr19:42791200-42794800	Strong transcription	Primary T helper cells fromperipheralblood	blood
41	chr19:42791200-42794800	Strong transcription	Fetal Intestine Large	intestine
42	chr19:42791200-42794800	Strong transcription	Placenta Amnion	Placenta Amnion
43	chr19:42791200-42796000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr19:42791200-42796200	Strong transcription	HUVEC	blood vessel
45	chr19:42791200-42796600	Strong transcription	Primary hematopoietic stem cells	blood
46	chr19:42791200-42798600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
47	chr19:42791200-42799000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr19:42791200-42799000	Strong transcription	HUES48 Cell Line	embryonic stem cell
49	chr19:42791200-42799000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
50	chr19:42791200-42799000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links