Variant report

Variant	rs352162
Chromosome Location	chr3:52252969-52252970
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr3:52251398..52253823-chr3:52256972..52258632,2	K562	blood:
2	chr3:52251268..52253019-chr3:52261280..52262997,2	MCF-7	breast:
3	chr3:52250996..52253546-chr3:52419538..52422445,2	K562	blood:
4	chr3:52251845..52253932-chr3:52273261..52274820,2	MCF-7	breast:
5	chr3:52251121..52253851-chr3:52256941..52260027,3	MCF-7	breast:
6	chr3:52252686..52254368-chr3:52255017..52257064,2	K562	blood:
7	chr3:52251508..52254087-chr3:52323193..52325029,2	MCF-7	breast:
8	chr3:52251118..52254493-chr3:52265556..52267197,3	K562	blood:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TLR9-1	chr3:52251032-52253028	NONHSAT089900

No data

Variant related genes	Relation type
ENSG00000243224	Chromatin interaction
ENSG00000168237	Chromatin interaction
ENSG00000247596	Chromatin interaction

Extended variants
information (count: 41 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs104903	0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1060330	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs11712164	0.95[CHB][hapmap];0.87[JPT][hapmap];0.87[ASN][1000 genomes]
rs11717383	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs164640	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs181274	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs187084	1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs352139	1.00[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.86[MKK][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352140	0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352158	0.89[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs352161	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs352163	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs352165	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs352166	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352167	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs352168	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352169	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs352170	0.89[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs352171	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353547	0.81[CHB][hapmap]
rs353551	0.90[CHB][hapmap];0.90[JPT][hapmap];0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs411457	0.89[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs524986	0.92[CEU][hapmap];0.91[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs610060	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs614288	0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6445358	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs6802320	0.90[ASN][1000 genomes]
rs730050	0.82[JPT][hapmap]
rs7614727	0.81[CHB][hapmap];0.83[JPT][hapmap]
rs7622851	0.87[JPT][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	nsv519445	chr3:52004317-52367932	Bivalent/Poised TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active 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 miRNA miRNA target site	134 gene(s)	inside rSNPs	diseases
2	nsv984541	chr3:52055970-52285682	Genic enhancers Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
3	nsv470572	chr3:52123313-52350212	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	103 gene(s)	inside rSNPs	diseases
4	nsv460537	chr3:52148233-52290550	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
5	nsv590301	chr3:52148233-52290550	Enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
6	nsv508218	chr3:52155869-52290410	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
7	nsv834694	chr3:52178983-52335821	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	102 gene(s)	inside rSNPs	diseases
8	nsv834695	chr3:52199701-52400577	Enhancers Weak transcription Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	98 gene(s)	inside rSNPs	diseases
9	nsv876787	chr3:52236762-52367932	Genic enhancers Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
10	nsv876788	chr3:52247110-52367932	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	90 gene(s)	inside rSNPs	diseases
11	nsv876789	chr3:52247110-52575831	Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Enhancers Genic enhancers Active TSS 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 miRNA target site	117 gene(s)	inside rSNPs	diseases

mRNA abundance (count:13)

SNP	Gene	Cis/trans	Tissue	Source
rs352162	RBM6	cis	cerebellum	SCAN
rs352162	GNL3	cis	parietal	SCAN
rs352162	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs352162	NEK4	cis	parietal	SCAN
rs352162	SEMA3G	cis	cerebellum	SCAN
rs352162	ITIH4	cis	parietal	SCAN
rs352162	NT5DC2	cis	lymphoblastoid	seeQTL
rs352162	SEMA3G	cis	parietal	SCAN
rs352162	SPCS1	cis	parietal	SCAN
rs352162	FLJ12442	cis	multi-tissue	Pritchard
rs352162	NEK4	cis	cerebellum	SCAN
rs352162	GNL3	cis	cerebellum	SCAN
rs352162	DNAH1	cis	cerebellum	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52247200-52263000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52247800-52272200	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:52249000-52254800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:52249600-52253000	Enhancers	Primary hematopoietic stem cells	blood
5	chr3:52249600-52263400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr3:52249800-52254600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr3:52249800-52254600	Weak transcription	Dnd41	blood
8	chr3:52249800-52262400	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr3:52249800-52262400	Weak transcription	Aorta	Aorta
10	chr3:52250000-52253000	Enhancers	Pancreas	Pancrea
11	chr3:52250000-52254000	Enhancers	Right Ventricle	heart
12	chr3:52250000-52254600	Weak transcription	HUES6 Cell Line	embryonic stem cell
13	chr3:52250000-52256800	Enhancers	Fetal Muscle Leg	muscle
14	chr3:52250000-52261400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr3:52250000-52261800	Weak transcription	Brain Germinal Matrix	brain
16	chr3:52250000-52262200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr3:52250000-52262600	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr3:52250200-52253000	Enhancers	Small Intestine	intestine
19	chr3:52250200-52255000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr3:52250200-52257800	Enhancers	Fetal Muscle Trunk	muscle
21	chr3:52250200-52262800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:52250400-52253400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr3:52250400-52253600	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr3:52250400-52253800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:52250400-52255200	Enhancers	Fetal Stomach	stomach
26	chr3:52250600-52253000	Enhancers	Thymus	Thymus
27	chr3:52250600-52253200	Enhancers	Primary monocytes fromperipheralblood	blood
28	chr3:52250600-52253200	Enhancers	Fetal Kidney	kidney
29	chr3:52250600-52253400	Enhancers	NH-A	brain
30	chr3:52250600-52253600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
31	chr3:52250600-52253600	Enhancers	Esophagus	oesophagus
32	chr3:52250600-52253800	Enhancers	Right Atrium	heart
33	chr3:52250600-52254000	Enhancers	Left Ventricle	heart
34	chr3:52250600-52254000	Enhancers	Lung	lung
35	chr3:52250600-52254000	Enhancers	Placenta Amnion	Placenta Amnion
36	chr3:52250600-52254000	Enhancers	K562	blood
37	chr3:52250600-52255400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr3:52250600-52255400	Enhancers	Fetal Lung	lung
39	chr3:52250600-52255400	Enhancers	Placenta	Placenta
40	chr3:52250600-52257000	Enhancers	Breast Myoepithelial Primary Cells	Breast
41	chr3:52250600-52257600	Genic enhancers	Primary B cells from cord blood	blood
42	chr3:52250600-52258200	Genic enhancers	Primary B cells from peripheral blood	blood
43	chr3:52250800-52253000	Enhancers	Fetal Thymus	thymus
44	chr3:52250800-52253200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:52250800-52253200	Enhancers	Sigmoid Colon	Sigmoid Colon
46	chr3:52250800-52253400	Genic enhancers	GM12878-XiMat	blood
47	chr3:52251000-52255200	Enhancers	Stomach Mucosa	stomach
48	chr3:52251000-52261800	Weak transcription	Fetal Brain Female	brain
49	chr3:52251000-52266600	Weak transcription	Fetal Brain Male	brain
50	chr3:52251200-52253000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links