Variant report

Variant	rs871776
Chromosome Location	chr2:64455674-64455675
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:64368361..64371459-chr2:64452988..64456076,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-LGALSL-2	chr2:64455337-64455710	NONHSAT071099

Variant related genes	Relation type
ENSG00000225889	Chromatin interaction

Extended variants
information (count: 61 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs1019684	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1019685	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1019686	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1025209	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1025210	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10496110	0.81[CEU][hapmap]
rs1365482	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1529101	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1582792	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1816618	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1963382	0.87[EUR][1000 genomes]
rs1969561	0.84[ASN][1000 genomes]
rs2059634	0.80[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2247947	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2251764	0.92[CEU][hapmap];0.89[GIH][hapmap];0.85[EUR][1000 genomes]
rs2433386	0.82[EUR][1000 genomes]
rs2433387	0.82[EUR][1000 genomes]
rs2555425	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2555426	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2555434	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2555436	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2555437	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2555438	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2555441	0.85[EUR][1000 genomes]
rs2555442	0.87[CEU][hapmap];0.89[YRI][hapmap];0.84[EUR][1000 genomes]
rs2698523	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2698524	0.84[EUR][1000 genomes]
rs2698525	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2698526	0.83[EUR][1000 genomes]
rs2698532	0.86[ASN][1000 genomes]
rs2698541	0.92[CEU][hapmap];0.89[GIH][hapmap];0.89[TSI][hapmap];0.87[EUR][1000 genomes]
rs2698542	0.83[ASN][1000 genomes]
rs2698543	0.86[EUR][1000 genomes]
rs2951018	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6750096	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs869739	0.83[EUR][1000 genomes]
rs890481	0.83[EUR][1000 genomes]
rs890482	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531376	chr2:64094322-64521876	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
2	nsv1013132	chr2:64235175-64631084	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	esv2757803	chr2:64253005-64539556	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	esv2759055	chr2:64253005-64539556	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv428396	chr2:64253005-64539556	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
6	esv34698	chr2:64312142-64521366	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	esv34955	chr2:64312182-64521290	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv834243	chr2:64316514-64476935	ZNF genes & repeats Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1006553	chr2:64339907-64764771	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
10	nsv9957	chr2:64341714-64518231	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
11	esv13275	chr2:64342247-64515169	Flanking Active TSS Weak transcription Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
12	nsv1012905	chr2:64342469-64508983	Active TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
13	nsv1013735	chr2:64342469-64512286	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
14	esv3693324	chr2:64342469-64513207	Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
15	nsv999608	chr2:64342469-64517459	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
16	nsv1000390	chr2:64343861-64512286	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
17	esv2756924	chr2:64349202-64521290	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
18	nsv1004574	chr2:64360195-64478171	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer 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	19 gene(s)	inside rSNPs	diseases
19	nsv1004899	chr2:64369300-64513607	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer 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	24 gene(s)	inside rSNPs	diseases
20	nsv535769	chr2:64369300-64513607	Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
21	nsv1015084	chr2:64369734-64512286	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
22	nsv874237	chr2:64402689-64479060	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
23	nsv1005492	chr2:64452441-64588323	Bivalent/Poised TSS Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs871776	PEX13	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:64454800-64456200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:64454800-64456400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr2:64454800-64456400	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
4	chr2:64454800-64456400	Flanking Active TSS	Primary B cells from cord blood	blood
5	chr2:64455000-64455800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:64455000-64455800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
7	chr2:64455000-64455800	Bivalent/Poised TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:64455000-64455800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr2:64455000-64455800	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr2:64455000-64455800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
11	chr2:64455000-64455800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
12	chr2:64455000-64455800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:64455000-64455800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:64455000-64455800	Active TSS	Aorta	Aorta
15	chr2:64455000-64455800	Active TSS	Brain Hippocampus Middle	brain
16	chr2:64455000-64455800	Active TSS	Brain Substantia Nigra	brain
17	chr2:64455000-64455800	Active TSS	Colonic Mucosa	Colon
18	chr2:64455000-64455800	Flanking Active TSS	Fetal Lung	lung
19	chr2:64455000-64455800	Flanking Bivalent TSS/Enh	HepG2	liver
20	chr2:64455000-64456000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
21	chr2:64455000-64456000	Flanking Active TSS	Primary B cells from peripheral blood	blood
22	chr2:64455000-64456000	Flanking Active TSS	Primary T cells fromperipheralblood	blood
23	chr2:64455000-64456000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr2:64455000-64456000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr2:64455000-64456000	Active TSS	Muscle Satellite Cultured Cells	--
26	chr2:64455000-64456000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr2:64455000-64456000	Flanking Active TSS	Liver	Liver
28	chr2:64455000-64456000	Active TSS	Brain Cingulate Gyrus	brain
29	chr2:64455000-64456000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
30	chr2:64455000-64456000	Active TSS	Duodenum Mucosa	Duodenum
31	chr2:64455000-64456000	Active TSS	Pancreatic Islets	Pancreatic Islet
32	chr2:64455000-64456000	Active TSS	Ovary	ovary
33	chr2:64455000-64456000	Active TSS	Psoas Muscle	Psoas
34	chr2:64455000-64456000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
35	chr2:64455000-64456000	Active TSS	Right Ventricle	heart
36	chr2:64455000-64456000	Active TSS	Skeletal Muscle Female	skeletal muscle
37	chr2:64455000-64456000	Flanking Bivalent TSS/Enh	A549	lung
38	chr2:64455000-64456000	Flanking Active TSS	HUVEC	blood vessel
39	chr2:64455000-64456200	Flanking Active TSS	H1 Cell Line	embryonic stem cell
40	chr2:64455000-64456200	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr2:64455000-64456200	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr2:64455000-64456200	Active TSS	Fetal Intestine Small	intestine
43	chr2:64455000-64456200	Flanking Active TSS	Fetal Muscle Leg	muscle
44	chr2:64455000-64456200	Flanking Active TSS	Fetal Thymus	thymus
45	chr2:64455000-64456200	Active TSS	Right Atrium	heart
46	chr2:64455000-64456200	Active TSS	Skeletal Muscle Male	skeletal muscle
47	chr2:64455000-64456200	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr2:64455000-64456200	Flanking Bivalent TSS/Enh	Dnd41	blood
49	chr2:64455000-64456200	Flanking Active TSS	GM12878-XiMat	blood
50	chr2:64455000-64456200	Flanking Active TSS	NH-A	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links