Variant report

Variant	rs4849166
Chromosome Location	chr2:113939763-113939764
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:4)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:113938786-113939775	GM12892	blood:	n/a	n/a
2	POLR2A	chr2:113938906-113939989	GM12891	blood:	n/a	n/a
3	POLR2A	chr2:113938859-113940095	GM12892	blood:	n/a	n/a
4	POLR2A	chr2:113938764-113940070	GM12878	blood:	n/a	n/a
5	POLR2A	chr2:113938930-113939932	GM12892	blood:	n/a	n/a
6	POLR2A	chr2:113938740-113941821	GM12891	blood:	n/a	n/a
7	POLR2A	chr2:113938755-113940185	HL-60	blood:	n/a	n/a

No data

(count:4 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:113933965..113936589-chr2:113937925..113940404,2	MCF-7	breast:
2	chr2:113914767..113917449-chr2:113937885..113940587,3	MCF-7	breast:
3	chr2:113939010..113941209-chr2:113958366..113960535,2	K562	blood:
4	chr2:113839317..113841682-chr2:113938699..113940328,2	K562	blood:

No data

Variant related genes	Relation type
PSD4	TF binding region
ENSG00000125637	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs12711762	0.91[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs12711765	0.89[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1975535	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2241976	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748914	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3791336	0.82[TSI][hapmap]
rs3791337	0.81[EUR][1000 genomes]
rs4848316	0.92[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4849163	0.91[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs4849167	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4849168	0.85[CEU][hapmap];0.91[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6737029	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6750127	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6760120	0.88[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.94[JPT][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6761202	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7595962	0.82[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997348	chr2:113688093-113986508	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv582711	chr2:113895516-113984503	Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv582712	chr2:113932431-113985170	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv874897	chr2:113935407-113944762	Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv874898	chr2:113935407-113954247	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv874899	chr2:113935407-113962071	Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs4849166	PSD4	cis	Whole Blood	GTEx
rs4849166	PSD4	cis	Esophagus Mucosa	GTEx
rs4849166	PSD4	cis	Esophagus Muscularis	GTEx
rs4849166	ZC3H8	cis	cerebellum	SCAN
rs4849166	LOC654433	cis	cerebellum	SCAN
rs4849166	PSD4	cis	Thyroid	GTEx
rs4849166	PSD4	cis	Stomach	GTEx
rs4849166	PSD4	cis	lung	GTEx
rs4849166	PSD4	cis	Skin Sun Exposed Lower leg	GTEx
rs4849166	LOC654433	cis	parietal	SCAN
rs4849166	PSD4	cis	multi-tissue	Pritchard

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113923000-113951800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:113923000-113956000	Weak transcription	HMEC	breast
3	chr2:113934200-113949000	Genic enhancers	Primary B cells from peripheral blood	blood
4	chr2:113934200-113956200	Weak transcription	Rectal Smooth Muscle	rectum
5	chr2:113934400-113940000	Genic enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:113934400-113948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr2:113934600-113940800	Genic enhancers	Fetal Thymus	thymus
8	chr2:113934600-113941000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
9	chr2:113934600-113946400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:113934800-113939800	Genic enhancers	Thymus	Thymus
11	chr2:113935200-113942800	Genic enhancers	Dnd41	blood
12	chr2:113935800-113939800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr2:113936200-113939800	Enhancers	Primary hematopoietic stem cells	blood
14	chr2:113936800-113940000	Enhancers	Liver	Liver
15	chr2:113936800-113940400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
16	chr2:113937600-113940000	Enhancers	Gastric	stomach
17	chr2:113937800-113939800	Enhancers	Fetal Intestine Large	intestine
18	chr2:113937800-113939800	Enhancers	Stomach Mucosa	stomach
19	chr2:113937800-113940400	Enhancers	Pancreas	Pancrea
20	chr2:113938000-113939800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
21	chr2:113938000-113945000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr2:113938200-113939800	Enhancers	Brain Anterior Caudate	brain
23	chr2:113938600-113939800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr2:113938800-113940200	Enhancers	Lung	lung
25	chr2:113938800-113945800	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:113939000-113939800	Transcr. at gene 5' and 3'	Primary T cells from cord blood	blood
27	chr2:113939000-113939800	Enhancers	Brain Substantia Nigra	brain
28	chr2:113939000-113939800	Genic enhancers	Rectal Mucosa Donor 29	rectum
29	chr2:113939000-113940000	Transcr. at gene 5' and 3'	Primary hematopoietic stem cells short term culture	blood
30	chr2:113939000-113940000	Enhancers	Sigmoid Colon	Sigmoid Colon
31	chr2:113939000-113944200	Genic enhancers	Spleen	Spleen
32	chr2:113939000-113944600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:113939200-113939800	Genic enhancers	Esophagus	oesophagus
34	chr2:113939200-113940000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr2:113939200-113940000	Enhancers	Brain Angular Gyrus	brain
36	chr2:113939200-113941000	Enhancers	Primary T helper naive cells from peripheral blood	blood
37	chr2:113939200-113945600	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr2:113939400-113939800	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
39	chr2:113939400-113940000	Weak transcription	Colonic Mucosa	Colon
40	chr2:113939400-113940400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr2:113939400-113941000	Enhancers	Primary T killer memory cells from peripheral blood	blood
42	chr2:113939400-113941000	Strong transcription	Fetal Intestine Small	intestine
43	chr2:113939400-113941400	Weak transcription	NHEK	skin
44	chr2:113939400-113945200	Strong transcription	Fetal Stomach	stomach
45	chr2:113939400-113945400	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
46	chr2:113939400-113946400	Genic enhancers	Primary T cells fromperipheralblood	blood
47	chr2:113939400-113946800	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
48	chr2:113939400-113948400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
49	chr2:113939400-113949000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:113939400-113956000	Weak transcription	Brain Cingulate Gyrus	brain

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