Variant report

Variant	rs1997604
Chromosome Location	chr3:146261504-146261505
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:146234591..146236203-chr3:146259470..146262375,2	MCF-7	breast:
2	chr3:146254115..146256698-chr3:146261297..146263941,3	MCF-7	breast:
3	chr17:7387396..7387925-chr3:146261229..146262098,2	Hela-S3	cervix:
4	chr3:146237235..146239692-chr3:146260498..146262293,2	K562	blood:
5	chr3:146251866..146257697-chr3:146260468..146262994,8	MCF-7	breast:
6	chr16:4475567..4476302-chr3:146260883..146261774,2	Hela-S3	cervix:
7	chr3:146234740..146236294-chr3:146259809..146262278,2	K562	blood:

Variant related genes	Relation type
ENSG00000174282	Chromatin interaction
ENSG00000262246	Chromatin interaction
ENSG00000188313	Chromatin interaction
ENSG00000181222	Chromatin interaction
ENSG00000103423	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1057481	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1061307	0.82[ASW][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes]
rs1079369	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[ASN][1000 genomes]
rs13064509	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.90[ASN][1000 genomes]
rs13069082	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs1373246	0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1443827	0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs16858420	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1882971	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1882972	0.88[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1882973	0.88[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1882974	0.88[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs1997601	0.88[CHB][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2120381	0.88[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.82[LWK][hapmap];0.89[MKK][hapmap];0.81[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2165948	0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587007	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2587008	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2587009	1.00[ASN][1000 genomes]
rs2587010	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587011	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587012	0.88[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2587013	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587014	0.88[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587015	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587016	0.93[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587017	1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587018	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2587021	0.82[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes]
rs2587023	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[ASN][1000 genomes]
rs2587024	0.82[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];0.94[JPT][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.81[YRI][hapmap];0.98[ASN][1000 genomes]
rs2587028	0.86[GIH][hapmap]
rs2587029	0.81[CEU][hapmap]
rs2609858	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2609860	0.87[ASW][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.80[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2609861	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2609862	0.99[ASN][1000 genomes]
rs2609864	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2609865	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2609866	0.88[ASW][hapmap];0.88[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.84[MEX][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2609867	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2688688	0.88[CHB][hapmap];0.94[JPT][hapmap];0.98[ASN][1000 genomes]
rs2738905	0.98[ASN][1000 genomes]
rs2738906	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2738907	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.84[MEX][hapmap];0.90[MKK][hapmap];0.85[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2738910	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2738911	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2738912	0.89[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2738915	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2738916	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2738918	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2738920	0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2738921	0.82[JPT][hapmap]
rs2738923	0.88[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.99[ASN][1000 genomes]
rs35214899	0.90[ASN][1000 genomes]
rs35309521	0.81[ASN][1000 genomes]
rs3773510	0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs67703040	0.85[ASN][1000 genomes]
rs7615988	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9289722	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.83[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs977758	0.87[ASN][1000 genomes]
rs9861142	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9865918	0.90[ASN][1000 genomes]
rs9876886	0.89[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.92[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	esv3448053	chr3:146186791-146262066	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
2	esv3523751	chr3:146186838-146261806	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
3	esv3523753	chr3:146186838-146261806	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
4	esv2496437	chr3:146186902-146262961	Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv1014493	chr3:146255594-146288414	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1997604	PLSCR1	cis	cerebellum	SCAN
rs1997604	CPB1	cis	cerebellum	SCAN
rs1997604	PLSCR1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:146257400-146261600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr3:146257400-146261600	Weak transcription	Spleen	Spleen
3	chr3:146257400-146261800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:146258000-146263200	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr3:146258400-146263200	Active TSS	Pancreatic Islets	Pancreatic Islet
6	chr3:146258600-146262000	Active TSS	Right Atrium	heart
7	chr3:146258800-146262200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:146258800-146263000	Active TSS	Brain Anterior Caudate	brain
9	chr3:146258800-146263000	Active TSS	Ovary	ovary
10	chr3:146259200-146262000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:146259200-146262800	Active TSS	Brain Hippocampus Middle	brain
12	chr3:146259200-146263200	Active TSS	Duodenum Smooth Muscle	Duodenum
13	chr3:146259200-146263200	Active TSS	Right Ventricle	heart
14	chr3:146259400-146261600	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
15	chr3:146259400-146263000	Active TSS	iPS-15b Cell Line	embryonic stem cell
16	chr3:146259600-146262800	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr3:146259600-146263000	Active TSS	iPS-20b Cell Line	embryonic stem cell
18	chr3:146259600-146263000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr3:146259800-146261600	Active TSS	Brain Cingulate Gyrus	brain
20	chr3:146259800-146261800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:146259800-146262800	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr3:146259800-146262800	Active TSS	Psoas Muscle	Psoas
23	chr3:146259800-146263000	Active TSS	Fetal Muscle Leg	muscle
24	chr3:146259800-146263200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr3:146259800-146263200	Active TSS	Colonic Mucosa	Colon
26	chr3:146260000-146261600	Flanking Active TSS	Dnd41	blood
27	chr3:146260000-146263000	Active TSS	Liver	Liver
28	chr3:146260000-146263000	Active TSS	Fetal Stomach	stomach
29	chr3:146260000-146263200	Active TSS	ES-I3 Cell Line	embryonic stem cell
30	chr3:146260000-146263200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr3:146260200-146262800	Active TSS	Brain Angular Gyrus	brain
32	chr3:146260200-146262800	Active TSS	Pancreas	Pancrea
33	chr3:146260200-146262800	Active TSS	Sigmoid Colon	Sigmoid Colon
34	chr3:146260200-146263000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr3:146260200-146263000	Active TSS	GM12878-XiMat	blood
36	chr3:146260200-146263000	Active TSS	Hela-S3	cervix
37	chr3:146260200-146263200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:146260400-146261800	Flanking Active TSS	Primary T cells from cord blood	blood
39	chr3:146260400-146263000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:146260400-146263000	Active TSS	Fetal Intestine Large	intestine
41	chr3:146260400-146263000	Active TSS	Fetal Intestine Small	intestine
42	chr3:146260400-146263000	Active TSS	Rectal Smooth Muscle	rectum
43	chr3:146260600-146261600	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
44	chr3:146260600-146261800	Flanking Active TSS	HUVEC	blood vessel
45	chr3:146260600-146262400	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:146260600-146263000	Active TSS	Fetal Adrenal Gland	Adrenal Gland
47	chr3:146260800-146261600	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
48	chr3:146260800-146261600	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
49	chr3:146260800-146261600	Enhancers	Fetal Heart	heart
50	chr3:146260800-146261600	Flanking Active TSS	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links